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

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Basic information

Entry
Database: PDB / ID: 7zmr
TitleCrystal structure of human RECQL5 helicase APO form in complex with engineered nanobody (Gluebody) G2*-011
Components
  • ATP-dependent DNA helicase Q5
  • Gluebody G2*-011
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: 3.3 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 G2*-011
C: Gluebody G2*-011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,21411
Polymers126,6034
Non-polymers6117
Water1,06359
1
A: ATP-dependent DNA helicase Q5
K: Gluebody G2*-011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5595
Polymers63,3012
Non-polymers2583
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ATP-dependent DNA helicase Q5
C: Gluebody G2*-011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,6556
Polymers63,3012
Non-polymers3544
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.890, 198.954, 172.926
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
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 G2*-011


Mass: 13764.168 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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.96 Å3/Da / Density % sol: 68.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M lithium sulfate -- 25% PEG3350 -- 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: Jan 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9119 Å / Relative weight: 1
ReflectionResolution: 3.04→99.54 Å / Num. obs: 38564 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.9 / Net I/σ(I): 3.4
Reflection shellResolution: 3.04→3.09 Å / Num. unique obs: 1907 / 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: 3.3→99.493 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.865 / SU B: 33.751 / SU ML: 0.516 / Cross valid method: FREE R-VALUE / ESU R Free: 0.545
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.292 1461 4.85 %
Rwork0.2431 28664 -
all0.245 --
obs-30125 99.861 %
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: 75.806 Å2
Baniso -1Baniso -2Baniso -3
1-0.017 Å20 Å2-0 Å2
2--0.069 Å20 Å2
3----0.086 Å2
Refinement stepCycle: LAST / Resolution: 3.3→99.493 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8695 0 25 59 8779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138980
X-RAY DIFFRACTIONr_bond_other_d0.0030.0178496
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.64312167
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5819524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49651144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.72521.223466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.878151521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2981572
X-RAY DIFFRACTIONr_chiral_restr0.0650.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022144
X-RAY DIFFRACTIONr_nbd_refined0.2180.21899
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.27761
X-RAY DIFFRACTIONr_nbtor_refined0.1670.24251
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.24192
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2212
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0340.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2830.226
X-RAY DIFFRACTIONr_nbd_other0.2670.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3220.25
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0330.21
X-RAY DIFFRACTIONr_mcbond_it4.897.9684539
X-RAY DIFFRACTIONr_mcbond_other4.897.9684538
X-RAY DIFFRACTIONr_mcangle_it8.00111.9455676
X-RAY DIFFRACTIONr_mcangle_other811.9455677
X-RAY DIFFRACTIONr_scbond_it4.6578.2724441
X-RAY DIFFRACTIONr_scbond_other4.6388.2694421
X-RAY DIFFRACTIONr_scangle_it7.83412.2726485
X-RAY DIFFRACTIONr_scangle_other7.80612.2676456
X-RAY DIFFRACTIONr_lrange_it14.462150.26536916
X-RAY DIFFRACTIONr_lrange_other14.463150.26636914
X-RAY DIFFRACTIONr_ncsr_local_group_10.1060.0513768
X-RAY DIFFRACTIONr_ncsr_local_group_20.10.053672
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.105650.05008
12BX-RAY DIFFRACTIONLocal ncs0.105650.05008
23KX-RAY DIFFRACTIONLocal ncs0.100330.05009
24CX-RAY DIFFRACTIONLocal ncs0.100330.05009
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
3.3-3.3860.3931080.38120950.38222110.5810.58199.63820.37
3.386-3.4780.358950.35620320.35621310.640.6899.81230.341
3.478-3.5790.378890.31519870.31720800.6930.77299.80770.297
3.579-3.6890.3271150.29319000.29520190.8180.82199.80190.277
3.689-3.810.2931010.28818720.28819750.8070.82199.89870.265
3.81-3.9430.3611170.26817880.27319080.7680.84299.84280.246
3.943-4.0920.3021070.2417170.24418260.8640.8799.89050.217
4.092-4.2590.314830.23617140.23917990.8530.89499.88880.21
4.259-4.4480.295930.20316010.20716950.8820.92299.9410.18
4.448-4.6640.294520.19615680.19916200.9090.9321000.17
4.664-4.9160.266670.20214850.20415520.9040.9341000.175
4.916-5.2140.308690.20814240.21314950.890.92499.86620.181
5.214-5.5720.278590.23213150.23413770.8920.91199.78210.199
5.572-6.0170.267620.22112470.22413090.910.9151000.195
6.017-6.5890.292360.22411670.22612030.9030.9081000.198
6.589-7.3630.323530.18410410.1910960.8840.93799.81750.164
7.363-8.4940.225550.1739160.1769730.9430.95499.79440.161
8.494-10.3840.188500.1867900.1868400.9590.9621000.179
10.384-14.6060.207390.2056190.2056580.9620.9621000.2
14.606-99.4930.264110.3263860.3254000.9370.9299.250.317

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