SAXSdb — 9x1p

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

DNA helicase

Thermococcus kodakarensis

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 Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain A； UniProt 1–592 Chain B； UniProt 1–592 Chain C； UniProt 1–592 Chain D； UniProt 1–592 Chain E； UniProt 1–592 Chain F； UniProt 1–592	Not recorded	;5'-3' nuclease, encoded next to Rad50 and Mre11 homologs ; × 2 （Q5JHL5） DNA × 1 DNA × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MN MANGANESE (II) ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 9X1P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X1L The cryo-EM structure of HerA-NurA complex with AMPPNP from Thermococcus kodakarensis Deposited 2025-10-02	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–592（592 aa） Chain B 1–592（592 aa） Chain C 1–592（592 aa） Chain D 1–592（592 aa） Chain E 1–592（592 aa） Chain F 1–592（592 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9X1M The cryo-EM structure of HerA-NurA complex with AMPPNP and dsDNA from Thermococcus kodakarensis Deposited 2025-10-02	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–592（592 aa） Chain B 1–592（592 aa） Chain C 1–592（592 aa） Chain D 1–592（592 aa） Chain E 1–592（592 aa） Chain F 1–592（592 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 MN MANGANESE (II) ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9X1N The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 1) Deposited 2025-10-02	Different ligand/ion	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–592（592 aa） Chain B 1–592（592 aa） Chain C 1–592（592 aa） Chain D 1–592（592 aa） Chain E 1–592（592 aa） Chain F 1–592（592 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MN MANGANESE (II) ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9X1O The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 2) Deposited 2025-10-02	Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain A 1–592（592 aa） Chain B 1–592（592 aa） Chain C 1–592（592 aa） Chain D 1–592（592 aa） Chain E 1–592（592 aa） Chain F 1–592（592 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MN MANGANESE (II) ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

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

View Construct and Data Evidence

UniProt name	Q5JHP7_THEKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–592； UniProt 1–592 Author chain B； PDBConstruct 1–592； UniProt 1–592 Author chain C； PDBConstruct 1–592； UniProt 1–592 Author chain D； PDBConstruct 1–592； UniProt 1–592 Author chain E； PDBConstruct 1–592； UniProt 1–592 Author chain F； PDBConstruct 1–592； UniProt 1–592

;5'-3' nuclease, encoded next to Rad50 and Mre11 homologs ;

Thermococcus kodakarensis

UniProt Q5JHL5

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 Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts	Chain G； UniProt 1–443 Chain H； UniProt 1–443	Mutation：D49A	DNA helicase × 6 （Q5JHP7） DNA × 1 DNA × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MN MANGANESE (II) ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 9X1P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9X1L The cryo-EM structure of HerA-NurA complex with AMPPNP from Thermococcus kodakarensis Deposited 2025-10-02	Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain G 1–443（443 aa） Chain H 1–443（443 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9X1M The cryo-EM structure of HerA-NurA complex with AMPPNP and dsDNA from Thermococcus kodakarensis Deposited 2025-10-02	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–443（443 aa） Chain H 1–443（443 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 6 MN MANGANESE (II) ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9X1N The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 1) Deposited 2025-10-02	Different ligand/ion	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–443（443 aa） Chain H 1–443（443 aa）	Mutation：D49A Mutation：D49A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 6 MN MANGANESE (II) ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9X1O The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 2) Deposited 2025-10-02	Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain G 1–443（443 aa） Chain H 1–443（443 aa）	Mutation：D49A Mutation：D49A	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MN MANGANESE (II) ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

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

View Construct and Data Evidence

UniProt name	Q5JHL5_THEKO
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–443； UniProt 1–443 Author chain H； PDBConstruct 1–443； UniProt 1–443

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	9x1p
Deposition date deposition_date	2025-10-02
Structure title title	The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 3)
Keywords keywords	HerA, Helicase, NurA, Nuclease, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	52.91 Å
Radius of gyration Rg (electron density) rg_electron	52.51 Å
Forward intensity I(0) i0	3405420000.00
Molecular weight molecular_weight	487440.0 kDa
Excluded volume excluded_volume	609730 Å³
Envelope volume envelope_volume	888680 Å³
Hydration-shell volume shell_volume	134960 Å³
Envelope diameter envelope_diameter	173.2 Å
Shell Rg shell_rg	60.87 Å
Envelope Rg envelope_rg	51.12 Å
Shape Rg shape_rg	52.55 Å
Total Rg total_rg	52.61 Å
Total atoms total_atoms	34280
Residues n_residues	4284
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	170.7 Å
Rg (real space) rg_real	52.73 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	3.4050e+09
I(0) uncertainty (real space) i0_real_error	6.5980e+07
Rg (reciprocal space) rg_reciprocal	53.05 Å
I(0) (reciprocal space) i0_reciprocal	3407000000.0000
Solution quality estimate total_estimate	0.8119
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.6 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	546700000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	DNA helicase
Molecular weight formula_weight	66118.1 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	34280

MRIAEDINKPVGIVTGEATVSSFQFYAHPDTDLKFGDFVVARLCKEAKDQNCRWGENEEGVEWVIGTIRGLKNINWLLSEGKSTYTSLELDIREYGESIGENEALIVTVHVLGKVQLNGEKAEVVPTRVPVPNGNRVYLASSDLLRAIYYGGNGYIELGRLIIREDVPVYLNVNELVSRHFAILAVTGAGKSNTVSVMLWKLVEELGGTVIVLDPHGDYTKLSLPGTGREYVNLIEAKIRPEAMDGEELADLMEIQSNASIQRSYLLRAWDTVLHENQGIGGREAVKLVHDLLQRWASEGGGTYWDPHAGQYRDLGEIKSAEKETIMRLTMKVSRFLRNYGHLLSSEDIVALIEPGKVNVIDLGPLDEGQMKLVVAKFLEKVFETRMDYEKARKRLDYLRTAYSSNISAVSDEINELEEFLRGVEKNYPALAEPVMVIVEEAHIFAPHGEKGGAVRILGRIAREGRKFGVGLGLVSQRPSRLSEDVLSQTNTKIIMRIVNPNDQQYVVRASEQVSGELMSDIAGLGKGEAVIVGQAISLPALVKIYNFKALGGNYGGEDIGAVERWLERKRRELEEKEKEEMYEEEGIEVDF

来源 Source

来源生物 organism	Thermococcus kodakarensis
NCBI Class编号 ncbi_taxonomy_id	311400
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;5'-3' nuclease, encoded next to Rad50 and Mre11 homologs ;
Molecular weight formula_weight	50991.7 kDa
Mutation mutation	D49A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MYRLIDRRSVDRIKALLERGYREAESKLAEIEWKPLPKERKQTRVYAVAGSQGKQRLSGTIFYAVSSYAFGNGPAYRLVYTNAMLYNQGISDQIIRLQMETLENKLGYLSAKLGDVDYVMMDGTLTGSLTRPPVYPESVKGLTTIENALGKGKLKELVKKFVSLLDEHYKELEDGLREKGKINGNVILADEKLEEFEEFYKAMKGYKVRDFAGTTPRGIKISRATIDEYLKGRKSAEEIFQELLNEYGEERELSLDDARNAVHVVLGYLEYLYSLEKLLRLNLVYVAKSFYNRKLTQKLGIDIVDVPYLDAYLRKRFGEEIPGYFIITQGGKAISHKMPKVLRETFPLVEHYIEHGVPMAYVRTMKGGVIYLLQSNREVDDDLLSEILWHESNGYFRPLQRAHEGVKIEKKAFEAELKALLNIIKAESPELRVFLKYGRSPLE

来源 Source

来源生物 organism	Thermococcus kodakarensis
NCBI Class编号 ncbi_taxonomy_id	311400
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	DNA
Molecular weight formula_weight	4026.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

AAAAAAAAAAAAA

Entity 4 Entity 4 polymer

Description description	DNA
Molecular weight formula_weight	3909.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TTTTTTTTTTTTT

Entity 5 Entity 5 non-polymer

Description description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	3

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

Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	96354

fit	/app/data/saxs_computation/x1/9x1p/9x1p.fit
pddf	/app/data/pr_computation/x1/9x1p/9x1p.pr.out
profile	/app/data/saxs_computation/x1/9x1p/9x1p.dat

The cryo-EM structure of HerA-NurA complex with ATPgammaS and dsDNA from Thermococcus kodakarensis (State 3)

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

DNA helicase

State in the Current Structure

Other States of the Same Protein in the Database

;5'-3' nuclease, encoded next to Rad50 and Mre11 homologs ;

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 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

Entity 7 Entity 7 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)