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

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Basic information

Entry
Database: PDB / ID: 7zmp
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G3-055
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G3-055
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 / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication ...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 / DNA 3'-5' helicase / transcription preinitiation complex / DNA metabolic process / negative regulation of transcription elongation by RNA polymerase II / DNA unwinding involved in DNA replication / RNA polymerase II complex binding / 3'-5' DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / DNA helicase activity / isomerase activity / helicase activity / replication fork / double-strand break repair via homologous recombination / cellular response to xenobiotic stimulus / chromosome / mitotic cell cycle / DNA replication / cell division / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / 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 / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain ...RecQ helicase-like 5 / RecQ helicase protein-like 5 (RecQ5) / 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 / DEAD/DEAH box helicase domain / 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 nucleoside triphosphate hydrolase
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: 3.626 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

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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 G3-055
C: Gluebody G3-055
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5476
Polymers126,4164
Non-polymers1312
Water1,51384
1
A: ATP-dependent DNA helicase Q5
C: Gluebody G3-055
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2743
Polymers63,2082
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-8 kcal/mol
Surface area26420 Å2
MethodPISA
2
B: ATP-dependent DNA helicase Q5
K: Gluebody G3-055
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,2743
Polymers63,2082
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-7 kcal/mol
Surface area26330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.109, 159.267, 220.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32K
42C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTRPTRPAA12 - 4534 - 445
21PROPROTRPTRPBB12 - 4534 - 445
32GLNGLNSERSERKC1 - 1244 - 127
42GLNGLNSERSERCD1 - 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 G3-055


Mass: 13670.980 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 6.25 Å3/Da / Density % sol: 80.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4M sodium malonate

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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: 3.626→129.07 Å / Num. obs: 36355 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 1 / Net I/σ(I): 3.9
Reflection shellResolution: 3.63→3.69 Å / Num. unique obs: 1772 / CC1/2: 0.2

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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: 3.626→129.017 Å / Cor.coef. Fo:Fc: 0.833 / Cor.coef. Fo:Fc free: 0.779 / SU B: 58.037 / SU ML: 0.789 / Cross valid method: FREE R-VALUE / ESU R Free: 0.67
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3594 1808 4.997 %
Rwork0.3322 34377 -
all0.334 --
obs-36185 99.59 %
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: 125.931 Å2
Baniso -1Baniso -2Baniso -3
1-0.787 Å2-0 Å20 Å2
2---0.234 Å2-0 Å2
3----0.553 Å2
Refinement stepCycle: LAST / Resolution: 3.626→129.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8640 0 0 84 8724
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138859
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178335
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.64112021
X-RAY DIFFRACTIONr_angle_other_deg1.1861.57919191
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97151149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.49921.716437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.312151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6731561
X-RAY DIFFRACTIONr_chiral_restr0.0510.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022068
X-RAY DIFFRACTIONr_nbd_refined0.2210.21974
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.27547
X-RAY DIFFRACTIONr_nbtor_refined0.1590.24146
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2222
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0540.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1410.223
X-RAY DIFFRACTIONr_nbd_other0.2270.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3940.24
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_mcbond_it8.70713.2974548
X-RAY DIFFRACTIONr_mcbond_other8.70813.2974547
X-RAY DIFFRACTIONr_mcangle_it14.22419.9285682
X-RAY DIFFRACTIONr_mcangle_other14.22319.9275683
X-RAY DIFFRACTIONr_scbond_it7.95713.94311
X-RAY DIFFRACTIONr_scbond_other7.95613.94311
X-RAY DIFFRACTIONr_scangle_it13.3620.5566308
X-RAY DIFFRACTIONr_scangle_other13.35920.5556309
X-RAY DIFFRACTIONr_lrange_it21.252154.6379744
X-RAY DIFFRACTIONr_lrange_other21.253154.6299743
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0513671
X-RAY DIFFRACTIONr_ncsr_local_group_20.0660.053547
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.058540.05008
12BX-RAY DIFFRACTIONLocal ncs0.058540.05008
23KX-RAY DIFFRACTIONLocal ncs0.066240.0501
24CX-RAY DIFFRACTIONLocal ncs0.066240.0501
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
3.626-3.720.4371170.4624880.45926590.2270.21497.96920.451
3.72-3.8220.411350.41524010.41525490.4370.42999.490.411
3.822-3.9330.451170.41423840.41625160.4340.46899.40380.41
3.933-4.0540.3431150.38323390.38224650.6270.61799.55370.382
4.054-4.1860.3681340.35221850.35323300.6670.66599.52790.344
4.186-4.3330.3181030.33421900.33322980.7180.70999.78240.324
4.333-4.4970.3491020.29620970.29822090.8240.83499.54730.271
4.497-4.680.3141040.27120520.27321640.8490.86599.63030.25
4.68-4.8880.2971010.26519120.26620190.880.88499.70280.242
4.888-5.1260.3831040.30518570.30919610.8270.8531000.282
5.126-5.4030.3091110.29817650.29918790.8430.85599.84030.276
5.403-5.730.296770.32916930.32717720.8250.81899.88710.307
5.73-6.1250.387890.32116000.32416920.7980.82699.82270.3
6.125-6.6140.336830.30414810.30515640.8750.8591000.277
6.614-7.2430.369720.28213800.28614530.8320.87499.93120.257
7.243-8.0950.332530.29312700.29513240.8720.87699.92450.269
8.095-9.3410.312640.30111000.30211650.8820.88499.91420.281
9.341-11.4260.335610.3189640.31910270.8680.89399.80530.301
11.426-16.0960.296370.3557570.3537940.8830.8811000.34
16.096-129.0170.674280.4854620.4974930.640.77299.39150.455

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