7zml

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001

Method: X-RAY DIFFRACTION D_max: 149.8 Å Quality: GOOD

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

ATP-dependent DNA helicase Q5

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 11–453	Not recorded	Gluebody G1-001 × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350	Resolution 2.79 Å R-free 0.261
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 11–453	Not recorded	Gluebody G1-001 × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350	Resolution 2.79 Å R-free 0.261
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 11–453	Not recorded	Gluebody G1-001 × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350	Resolution 2.79 Å R-free 0.261
4	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 11–453	Not recorded	Gluebody G1-001 × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.9；293 K；0.1M bis-tris pH 5.9 -- 0.1M lithium sulfate -- 30% PEG3350	Resolution 2.79 Å R-free 0.261

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 7ZML	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BK0 Crystal structure of the KIX domain of human RECQL5 (domain-swapped dimer) Deposited 2013-04-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 515–620（106 aa） Fragment：KIX DOMAIN, RESIDUES 515-620 Chain B 515–620（106 aa） Fragment：KIX DOMAIN, RESIDUES 515-620	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；0.2 M NACL, 0.1 M SODIUM/POTASSIUM PHOSPHATE PH 6.2, 50% PEG 200	Resolution 1.90 Å R-free 0.234
5LB3 Crystal structure of human RECQL5 helicase in complex with ADP/Mg. Deposited 2016-06-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；23% PEG6K, 0.15M lithium chloride, 2.5% ethylene glycol	Resolution 1.80 Å R-free 0.234
5LB3 Crystal structure of human RECQL5 helicase in complex with ADP/Mg. Deposited 2016-06-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；23% PEG6K, 0.15M lithium chloride, 2.5% ethylene glycol	Resolution 1.80 Å R-free 0.234
5LB5 Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form). Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 10–453（444 aa）	Not recorded	ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 23% PEG3350, 0.1M sodium chloride	Resolution 2.00 Å R-free 0.282
5LB5 Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form). Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 10–453（444 aa）	Not recorded	ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 23% PEG3350, 0.1M sodium chloride	Resolution 2.00 Å R-free 0.282
5LB5 Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form). Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 10–453（444 aa）	Not recorded	ZN ZINC ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 23% PEG3350, 0.1M sodium chloride	Resolution 2.00 Å R-free 0.282
5LB5 Crystal structure of human RECQL5 helicase in complex with ADP/Mg (tricilinc form). Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 10–453（444 aa）	Not recorded	ZN ZINC ION × 1 DMS DIMETHYL SULFOXIDE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1M tris pH 7.5, 23% PEG3350, 0.1M sodium chloride	Resolution 2.00 Å R-free 0.282
5LB8 Crystal structure of human RECQL5 helicase APO form. Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–526（516 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；17.5% Peg 3350, 0.2M Potassium Thiocyanate, 0.1M Hepes pH 7.0, 10% ethelene glycol	Resolution 3.40 Å R-free 0.322
5LB8 Crystal structure of human RECQL5 helicase APO form. Deposited 2016-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 11–526（516 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；17.5% Peg 3350, 0.2M Potassium Thiocyanate, 0.1M Hepes pH 7.0, 10% ethelene glycol	Resolution 3.40 Å R-free 0.322
5LBA Crystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening. Deposited 2016-06-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 11–453（443 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DMS DIMETHYL SULFOXIDE × 1 6SV 1-cyclohexyl-3-[[(2~{R})-oxolan-2-yl]methyl]urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M tris pH 9.0 -- 29% PEG3350 -- 0.1M sodium chloride	Resolution 2.50 Å R-free 0.303
5LBA Crystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening. Deposited 2016-06-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–453（443 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M tris pH 9.0 -- 29% PEG3350 -- 0.1M sodium chloride	Resolution 2.50 Å R-free 0.303
5LBA Crystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening. Deposited 2016-06-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 11–453（443 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M tris pH 9.0 -- 29% PEG3350 -- 0.1M sodium chloride	Resolution 2.50 Å R-free 0.303
5LBA Crystal structure of human RECQL5 helicase in complex with DSPL fragment(1-cyclohexyl-3-(oxolan-2-ylmethyl)urea, SGC - Diamond XChem I04-1 fragment screening. Deposited 2016-06-15	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 11–453（443 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1M tris pH 9.0 -- 29% PEG3350 -- 0.1M sodium chloride	Resolution 2.50 Å R-free 0.303
7ZMM Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5	Resolution 2.50 Å R-free 0.281
7ZMM Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5	Resolution 2.50 Å R-free 0.281
7ZMM Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5	Resolution 2.50 Å R-free 0.281
7ZMM Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2-001 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M sodium chloride -- 25% PEG3350 -- 0.1M bis-tris pH 6.5	Resolution 2.50 Å R-free 0.281
7ZMN Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-048 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate -- 0.1M HEPES pH 7.5	Resolution 3.20 Å R-free 0.275
7ZMN Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-048 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate -- 0.1M HEPES pH 7.5	Resolution 3.20 Å R-free 0.275
7ZMO Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-052 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1M ammonium sulfate -- 0.5% PEG8000 -- 0.1M HEPES pH 7.0	Resolution 3.75 Å R-free 0.306
7ZMO Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-052 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1M ammonium sulfate -- 0.5% PEG8000 -- 0.1M HEPES pH 7.0	Resolution 3.75 Å R-free 0.306
7ZMP Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-055 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4M sodium malonate	Resolution 3.63 Å R-free 0.359
7ZMP Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-055 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4M sodium malonate	Resolution 3.63 Å R-free 0.359
7ZMQ Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-006 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M lithium sulfate -- 25% PEG3350 -- 0.1M tris pH 8.5	Resolution 2.70 Å R-free 0.258
7ZMQ Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-006 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M lithium sulfate -- 25% PEG3350 -- 0.1M tris pH 8.5	Resolution 2.70 Å R-free 0.258
7ZMR Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-011 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M lithium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 3.30 Å R-free 0.292
7ZMR Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-011 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M lithium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 3.30 Å R-free 0.292
7ZMS Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G4-043 Deposited 2022-04-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 12–453（442 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M sodium chloride -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 2.70 Å R-free 0.276
7ZMT Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium formate -- 20% PEG3350	Resolution 2.30 Å R-free 0.291
7ZMT Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 Deposited 2022-04-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium formate -- 20% PEG3350	Resolution 2.30 Å R-free 0.291
7ZMV Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M ammonium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.275
7ZMV Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M ammonium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.275
7ZMV Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M ammonium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.275
7ZMV Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G5-006 Deposited 2022-04-19	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 11–453（443 aa）	Not recorded	ZN ZINC ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.2M ammonium sulfate -- 25% PEG3350 -- 0.1M HEPES pH 7.5	Resolution 2.00 Å R-free 0.275
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain R 1–650（650 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain R 1–650（650 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain R 1–650（650 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å
8RL5 DNA helicase RECQL5 in complex with homo Di-Gluebody G5-006 Deposited 2024-01-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 12–453（442 aa） Chain B 12–453（442 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.79 Å
8RL6 DNA helicase RECQL5 in complex with homo Di-Gluebody G5-006 - RECQL5 local refinement Deposited 2024-01-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 12–453（442 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
8RL9 RECQL5:sfGFP hetero dimer assembled by Di-Gluebody Deposited 2024-01-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 12–453（442 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8RLA RECQL5:sfGFP hetero dimer assembled by Di-Gluebody - RECQL5 local refinement Deposited 2024-01-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 12–453（442 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain U 1–991（991 aa）	Mutation：D157A	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9EI2 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to an apo RECQL5 helicase (RECQL5 IRI Module focused-classified) Deposited 2024-11-25	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain U 1–991（991 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain U 1–991（991 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain U 1–991（991 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9HVO Structure of the transcribing Pol II-RECQL5 complex Deposited 2024-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: 16-meric	Chain O 1–991（991 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 100 mM NaCl, 3 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
9HVQ Structure of the transcribing Pol II-DSIF-PAF-SPT6-RECQL5 complex Deposited 2024-12-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric	Chain O 1–991（991 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.00 Å
9HWG Structure of the transcribing Pol II-TCR-RECQL5 complex Deposited 2025-01-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric	Chain O 1–991（991 aa）	Not recorded	ZN ZINC ION × 10 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å

28 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RECQ5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–445； UniProt 11–453 Author chain B； PDBConstruct 3–445； UniProt 11–453 Author chain C； PDBConstruct 3–445； UniProt 11–453 Author chain D； PDBConstruct 3–445； UniProt 11–453

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7zml
Deposition date deposition_date	2022-04-19
Structure title title	Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001
Keywords keywords	Helicase, Apo form, Nanobody complex, 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	46.85 Å
Radius of gyration Rg (electron density) rg_electron	46.85 Å
Forward intensity I(0) i0	947184000.00
Molecular weight molecular_weight	251000.0 kDa
Excluded volume excluded_volume	312930 Å³
Envelope volume envelope_volume	442790 Å³
Hydration-shell volume shell_volume	79716 Å³
Envelope diameter envelope_diameter	158.0 Å
Shell Rg shell_rg	50.62 Å
Envelope Rg envelope_rg	45.30 Å
Shape Rg shape_rg	46.81 Å
Total Rg total_rg	47.10 Å
Total atoms total_atoms	17607
Residues n_residues	2283
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	149.8 Å
Rg (real space) rg_real	46.74 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	9.4720e+08
I(0) uncertainty (real space) i0_real_error	1.3070e+07
Rg (reciprocal space) rg_reciprocal	46.85 Å
I(0) (reciprocal space) i0_reciprocal	947300000.0000
Solution quality estimate total_estimate	0.8737
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.271
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	47000000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.892; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.694

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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	ATP-dependent DNA helicase Q5
Molecular weight formula_weight	49537.2 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17730

SMDPERRVRSTLKKVFGFDSFKTPLQESATMAVVKGNKDVFVCMPTGAGKSLCYQLPALLAKGITIVVSPLIALIQDQVDHLLTLKVRVSSLNSKLSAQERKELLADLEREKPQTKILYITPEMAASSSFQPTLNSLVSRHLLSYLVVDEAHCVSQWGHDFRPDYLRLGALRSRLGHAPCVALTATATPQVQEDVFAALHLKKPVAIFKTPCFRANLFYDVQFKELISDPYGNLKDFCLKALGQEADKGLSGCGIVYCRTREACEQLAIELSCRGVNAKAYHAGLKASERTLVQNDWMEEKVPVIVATISFGMGVDKANVRFVAHWNIAKSMAGYYQESGRAGRDGKPSWCRLYYSRNDRDQVSFLIRKEVAKLQEKRGNKASDKATIMAFDALVTFCEELGCRHAAIAKYFGDALPACAKGCDHCQNPTAVRRRLEALERSSSW

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Gluebody G1-001
Molecular weight formula_weight	14347.8 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K,E,F,G

QVQLQESGGGLVQAGGSLRLSCAASGSIFSINRMGWYRQAPGKQRELVAAITSGGSTNYAYSVKGRFTISRDNAKNTVYLQMNSLKPEDTAIYYCEAYGTYTLAPTGEGEYDDYWGQGTQVTVSAAENLYFQ

来源 Source

来源生物 organism	Lama glama
NCBI Class编号 ncbi_taxonomy_id	9844
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	19

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7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	7zmlA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	7zmlE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7zmlF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7zmlG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7zmlK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	75.740 Å
Unit-cell length b length_b	185.530 Å
Unit-cell length c length_c	101.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.790 Å
Low-resolution limit resolution_low	96.351 Å
R factor r_factor	—
R_work r_work	0.2238
R_free r_free	0.2610

fit	/app/data/saxs_computation/zm/7zml/7zml.fit
pddf	/app/data/pr_computation/zm/7zml/7zml.pr.out
profile	/app/data/saxs_computation/zm/7zml/7zml.dat

Crystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G1-001

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

ATP-dependent DNA helicase Q5

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)