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- PDB-7zmn: Crystal structure of human RECQL5 helicase APO form in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7zmn
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-048
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G3-048
KeywordsHYDROLASE / Helicase / Apo form / Nanobody complex
Function / homology
Function and homology information


mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / RNA polymerase II complex binding ...mitotic DNA-templated DNA replication / chromosome separation / cellular response to camptothecin / four-way junction helicase activity / replication-born double-strand break repair via sister chromatid exchange / transcription preinitiation complex / DNA 3'-5' helicase / DNA metabolic process / 3'-5' DNA helicase activity / RNA polymerase II complex binding / negative regulation of transcription elongation by RNA polymerase II / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / replication fork / helicase activity / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / mitotic cell cycle / chromosome / DNA replication / cell division / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ATP-dependent DNA helicase Q5
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsYe, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Aitkenhead, H. / Bountra, C. / Gileadi, O. / von Delft, F.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Scholarship Council China
CitationJournal: To Be Published
Title: Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive crystal contacts
Authors: Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Wright, N.D. / Koekemoer, L. / Thompson, A. / Bezerra, G.A. / Yi, G. / Li, H. / Rangel, V.L. / Mamalis, D. / ...Authors: Ye, M. / Makola, M. / Newman, J.A. / Fairhead, M. / MacLean, E. / Krojer, T. / Wright, N.D. / Koekemoer, L. / Thompson, A. / Bezerra, G.A. / Yi, G. / Li, H. / Rangel, V.L. / Mamalis, D. / Aitkenhead, H. / Gilbert, R.J.C. / Duerr, K. / Davis, B.G. / Bountra, C. / Gileadi, O. / von Delft, F.
History
DepositionApr 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP-dependent DNA helicase Q5
B: ATP-dependent DNA helicase Q5
K: Gluebody G3-048
C: Gluebody G3-048
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9029
Polymers126,4834
Non-polymers4195
Water48627
1
A: ATP-dependent DNA helicase Q5
C: Gluebody G3-048
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4995
Polymers63,2412
Non-polymers2583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-30 kcal/mol
Surface area26140 Å2
MethodPISA
2
B: ATP-dependent DNA helicase Q5
K: Gluebody G3-048
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4034
Polymers63,2412
Non-polymers1612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1690 Å2
ΔGint-24 kcal/mol
Surface area26050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.503, 89.573, 259.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32K
42C

NCS domain segments:

Component-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA12 - 4514 - 443
21PROPROBB12 - 4514 - 443
32GLNGLNKC1 - 1244 - 127
42GLNGLNCD1 - 1244 - 127

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

#1: Protein ATP-dependent DNA helicase Q5 / DNA helicase / RecQ-like type 5 / RecQ5 / RecQ protein-like 5


Mass: 49537.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RECQL5, RECQ5 / Production host: Escherichia coli (E. coli) / References: UniProt: O94762, DNA helicase
#2: Antibody Gluebody G3-048


Mass: 13704.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2M ammonium sulfate -- 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9119 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 2.74→129.63 Å / Num. obs: 49418 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 1 / Net I/σ(I): 4.8
Reflection shellResolution: 2.74→2.79 Å / Num. unique obs: 2406 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LB5

5lb5


Resolution: 3.2→129.528 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.867 / SU B: 25.875 / SU ML: 0.42 / Cross valid method: FREE R-VALUE / ESU R Free: 0.487
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2746 1559 4.986 %
Rwork0.2419 29708 -
all0.244 --
obs-31267 99.535 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 69.309 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.037 Å20 Å2
3---0.047 Å2
Refinement stepCycle: LAST / Resolution: 3.2→129.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8686 0 17 27 8730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138957
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178469
X-RAY DIFFRACTIONr_angle_refined_deg1.541.64312145
X-RAY DIFFRACTIONr_angle_other_deg1.2621.57919477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.33351147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.08321.161465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.994151518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6071573
X-RAY DIFFRACTIONr_chiral_restr0.0630.21162
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022132
X-RAY DIFFRACTIONr_nbd_refined0.2130.21838
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.27722
X-RAY DIFFRACTIONr_nbtor_refined0.1630.24197
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.24166
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2170
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0470.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1960.228
X-RAY DIFFRACTIONr_nbd_other0.2460.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2290.26
X-RAY DIFFRACTIONr_mcbond_it5.1967.2284542
X-RAY DIFFRACTIONr_mcbond_other5.1957.2284541
X-RAY DIFFRACTIONr_mcangle_it8.37510.8255676
X-RAY DIFFRACTIONr_mcangle_other8.37410.8255677
X-RAY DIFFRACTIONr_scbond_it4.9857.6214414
X-RAY DIFFRACTIONr_scbond_other4.9887.6254402
X-RAY DIFFRACTIONr_scangle_it8.23911.2256451
X-RAY DIFFRACTIONr_scangle_other8.24511.2316434
X-RAY DIFFRACTIONr_lrange_it12.14183.1489658
X-RAY DIFFRACTIONr_lrange_other12.14283.1439657
X-RAY DIFFRACTIONr_ncsr_local_group_10.0890.0513762
X-RAY DIFFRACTIONr_ncsr_local_group_20.0690.053729
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.089030.05008
12BX-RAY DIFFRACTIONLocal ncs0.089030.05008
23KX-RAY DIFFRACTIONLocal ncs0.069020.0501
24CX-RAY DIFFRACTIONLocal ncs0.069020.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.2-3.2830.3521070.33321600.33422680.6880.72699.95590.296
3.283-3.3730.3551150.31620700.31822020.7820.7899.2280.272
3.373-3.4710.366860.32320890.32521890.7360.78699.36040.287
3.471-3.5770.3691070.28819810.29320960.7560.80799.61830.257
3.577-3.6950.307920.28119350.28320350.8490.84999.60690.253
3.695-3.8240.2971260.2618450.26319830.8770.87999.39490.227
3.824-3.9680.2761120.25418070.25519290.8970.89799.48160.226
3.968-4.130.239840.21817380.21918300.910.92399.56280.193
4.13-4.3140.227750.20116850.20217690.9320.93799.49120.175
4.314-4.5240.189760.18616260.18617080.9490.94799.64870.167
4.524-4.7690.222670.19615560.19716280.9440.93899.69290.18
4.769-5.0570.235960.20414240.20615240.9310.93599.73750.185
5.057-5.4060.283590.21413890.21714560.9240.9499.45050.194
5.406-5.8380.282620.26212880.26313550.9120.91999.6310.234
5.838-6.3940.312590.2811960.28112590.8320.8899.68230.252
6.394-7.1470.259650.19810740.20111440.920.94599.56290.18
7.147-8.2480.239540.1839690.18610260.9320.9599.70760.165
8.248-10.0920.234470.2048360.2058870.950.95699.5490.192
10.092-14.2290.19380.2046480.2036890.9760.97499.56460.198
14.229-129.5280.458320.393920.3954360.8060.87397.24770.367

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