SAXSdb — 6h57

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

Probable ATP-dependent RNA helicase DHR1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–1267	Not recorded	EDO 1,2-ETHANEDIOL × 14 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；278 K；0.2 M MgCl2; 0.1 M Tris pH 8.5 and 20% (w/v) PEG 8000	Resolution 2.30 Å R-free 0.245

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 6H57	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ZQD Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1 Deposited 2020-07-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 63 PDB declaration: 66-meric	Chain JD 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6ZQE Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-A (Poly-Ala) Deposited 2020-07-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric	Chain JD 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6ZQF Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala) Deposited 2020-07-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric	Chain JD 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
6ZQG Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C Deposited 2020-07-09	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric	Chain JD 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 39	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7AJU Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome) Deposited 2020-09-29	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric	Chain JD 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7D4I Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F) Deposited 2020-09-24	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric	Chain RZ 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7D5T Cryo-EM structure of 90S preribosome with inactive Utp24 (state F1) Deposited 2020-09-28	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric	Chain RZ 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.00 Å
7D63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C) Deposited 2020-09-29	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain RZ 1–1267（1267 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.30 Å
7MQJ Dhr1 Helicase Core Deposited 2021-05-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 379–1174（796 aa） Fragment：UNP residues 379-1174	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；PEG6000, HEPES, pH 7.0, magnesium chloride, ADP	Resolution 2.23 Å R-free 0.227
9N6Z SSU processome maturation and disassembly, State D Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain NS 1–1267（1267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.74 Å
9N70 SSU processome maturation and disassembly, State E Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain NS 1–1267（1267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.17 Å
9N72 SSU processome maturation and disassembly, State F Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric	Chain NS 1–1267（1267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.94 Å
9N73 SSU processome maturation and disassembly, State G Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 71 PDB declaration: 74-meric	Chain NS 1–1267（1267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.96 Å
9N74 SSU processome maturation and disassembly, State H Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 39 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å
9N75 SSU processome maturation and disassembly, State I Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 68-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 59 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9N76 SSU processome maturation and disassembly, State J Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 67-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 38 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9N77 SSU processome maturation and disassembly, State K Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 64-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 48 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9N78 SSU processome maturation and disassembly, State L Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 59-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.17 Å
9N79 SSU processome maturation and disassembly, State M Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9N7A SSU processome maturation and disassembly, State N Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 39-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
9N7B SSU processome maturation and disassembly, State O Deposited 2025-02-05	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric	Chain NS 1–1267（1267 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHR1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1267； UniProt 1–1267

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	6h57
Deposition date deposition_date	2018-07-24
Structure title title	Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis
Keywords keywords	protein, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	32.09 Å
Radius of gyration Rg (electron density) rg_electron	31.29 Å
Forward intensity I(0) i0	125499000.00
Molecular weight molecular_weight	91195.0 kDa
Excluded volume excluded_volume	115330 Å³
Envelope volume envelope_volume	150350 Å³
Hydration-shell volume shell_volume	40286 Å³
Envelope diameter envelope_diameter	115.3 Å
Shell Rg shell_rg	38.12 Å
Envelope Rg envelope_rg	31.22 Å
Shape Rg shape_rg	31.32 Å
Total Rg total_rg	31.78 Å
Total atoms total_atoms	6401
Residues n_residues	795
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	107.8 Å
Rg (real space) rg_real	32.05 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	1.2550e+08
I(0) uncertainty (real space) i0_real_error	1.9500e+06
Rg (reciprocal space) rg_reciprocal	32.07 Å
I(0) (reciprocal space) i0_reciprocal	125500000.0000
Solution quality estimate total_estimate	0.8905
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.6 Å
Skewness Skewness skewness	0.295
Kurtosis Kurtosis kurtosis	-0.356
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	31680000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.978

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Probable ATP-dependent RNA helicase DHR1
Molecular weight formula_weight	145171.4 kDa
EC 编号 ec_number	3.6.4.13
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	6697

MGTYRKRFNEKARSGHMAKLKELKRIRNKQFTRQDENDERVENPDSAPAESSTTEPNANAEILEPLTEEEKKMKKRKLQELFTPKESKVSRLKKKRLDKFIEHQLKREERKTIIGKLQDYKIDTSLLTSSKRLGEGRQTKKEEFKEALSLERQGRGNEQTNEILYEEYEPKVWDEYGEGGSSEDDDGEDDFEASFGSMPKPTDNEEKKSSGFIDHRPAKFGGSGLSFGFSNIKVINKESKTPKKKYNWRQRVEMEELKKHGKEDEMDFDTTSEDDDEEEDQEEEDKMHPSENPLEEVESADSETGSEKFDQNDVANEFKDWANQEIKKLEGRDQELVTPTLNIDYKPIIRKEDLDDGLQEAYVPINENSTRKAFYVEVSRSDEIQKARIQLPVFGEEHKIMEAIHHNDVVIICGETGSGKTTQVPQFLYEAGFGAEDSPDYPGMVGITQPRRVAAVSMAERVANELGDHGHKVGYQIRFDSTAKEDTKVKFMTDGVLLREMMHDFKLTKYSSIIIDEAHERNINTDILIGMLSRCVRLRAKLHKENPIEHKKLKLIIMSATLRVSDFSENKTLFPIAPPVLQVDARQFPVSIHFNRRTAFNYTDEAFRKTCKIHQKLPPGAILVFLTGQQEITHMVKRLRKEFPFKKNSKYNKDLETPVSKMGINSKTTDLEAEDIDFSVQVIDQDKFKSAIRYEEDEGNSGNGEDEEDEEEEGFEEVLTEGQTANDPLYVLPLYSLLPTKEQMRVFQKPPQGSRLCIVATNVAETSLTIPGVRYVVDSGRSKERKYNESNGVQSFEVGWVSKASANQRSGRAGRTGPGHCYRLYSSAVFEHDFEQFSKPEILRMPVESIVLQMKSMAIHNIINFPFPTPPDRVALSKAIQLLQYLGALDNKEMITEDGKKMSLFPLSPRFSKMLLVSDEKACLPYIVAIVSALSVGDPFINEFELGINEISRKPNPDENLDDKIREHDESTPGMDPELKKELRSKFYKSRSQFSKLDKFSDVFRLLSVVSAMDYVPKEQKEIFMKKNFLRGKLMEEIVKLRKQLMYIIKSNTSKENIAVVIRNEDLKSDIPSVIQIKLLKQMICAGFVDHVAVRADVLFPDDAKITNRTSIINIPYIPVLATRTPNIEDCFVYIHPTSILNNLGEMPPKYMLYYSLHLGGNNKTRMNTLCDIASTPLANIARKGLLLTYSKPLTGQGLKTVNLSPTERYCYVVPRFGSTVDNDLKIGWDLNPIAVHQKKQKGQWTVIKFITRKGFQTITGEEKEKK

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

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8. Citations (1)

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Unit-cell length a length_a	57.314 Å
Unit-cell length b length_b	115.800 Å
Unit-cell length c length_c	157.479 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.830 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2450

fit	/app/data/saxs_computation/h5/6h57/6h57.fit
pddf	/app/data/pr_computation/h5/6h57/6h57.pr.out
profile	/app/data/saxs_computation/h5/6h57/6h57.dat

Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis

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

Probable ATP-dependent RNA helicase DHR1

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

Diffraction experiment Diffraction