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- PDB-5mk5: Structures of DHBN domain of human BLM helicase -

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Basic information

Entry
Database: PDB / ID: 5mk5
TitleStructures of DHBN domain of human BLM helicase
ComponentsBloom syndrome protein
KeywordsHYDROLASE / helicase dimerization alpha-helix motif
Function / homology
Function and homology information


regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA/DNA annealing activity / telomere maintenance via semi-conservative replication / cellular response to camptothecin ...regulation of DNA-templated DNA replication / RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / forked DNA-dependent helicase activity / resolution of DNA recombination intermediates / 8-hydroxy-2'-deoxyguanosine DNA binding / telomeric D-loop binding / DNA/DNA annealing activity / telomere maintenance via semi-conservative replication / cellular response to camptothecin / G-quadruplex DNA unwinding / telomeric D-loop disassembly / t-circle formation / DNA double-strand break processing / Y-form DNA binding / negative regulation of cell division / DNA 3'-5' helicase / four-way junction helicase activity / G-quadruplex DNA binding / cellular response to hydroxyurea / lateral element / negative regulation of DNA recombination / Processive synthesis on the C-strand of the telomere / bubble DNA binding / Impaired BRCA2 binding to PALB2 / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / 3'-5' DNA helicase activity / Resolution of D-loop Structures through Holliday Junction Intermediates / DNA duplex unwinding / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / replication fork processing / nuclear chromosome / DNA unwinding involved in DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / response to X-ray / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / four-way junction DNA binding / DNA helicase activity / telomere maintenance / replication fork / helicase activity / molecular function activator activity / cellular response to ionizing radiation / double-strand break repair via homologous recombination / protein homooligomerization / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / PML body / Meiotic recombination / nuclear matrix / p53 binding / single-stranded DNA binding / protein complex oligomerization / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / DNA replication / DNA repair / DNA damage response / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / protein homodimerization activity / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain ...RecQ-like DNA helicase BLM, N-terminal domain / RecQ-like DNA helicase BLM, BDHCT-box associated domain / N-terminal region of Bloom syndrome protein / BDHCT-box associated domain on Bloom syndrome protein / BDHCT / BDHCT (NUC031) domain / RQC domain / RQC / RQC domain / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / HRDC domain superfamily / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / HRDC-like superfamily / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
IODIDE ION / : / RecQ-like DNA helicase BLM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsShi, J. / Chen, W.-F. / Zhang, B. / Fan, S.-H. / Ai, X. / Liu, N.-N. / Rety, S. / Xi, X.-G.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A helical bundle in the N-terminal domain of the BLM helicase mediates dimer and potentially hexamer formation.
Authors: Shi, J. / Chen, W.F. / Zhang, B. / Fan, S.H. / Ai, X. / Liu, N.N. / Rety, S. / Xi, X.G.
History
DepositionDec 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
SupersessionJun 23, 2021ID: 5M1V
Revision 1.3Jun 23, 2021Group: Advisory / Derived calculations
Category: pdbx_database_PDB_obs_spr / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bloom syndrome protein
B: Bloom syndrome protein
C: Bloom syndrome protein
D: Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,22227
Polymers25,5664
Non-polymers2,65523
Water2,414134
1
A: Bloom syndrome protein
B: Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,96412
Polymers12,7832
Non-polymers1,18110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-37 kcal/mol
Surface area6790 Å2
MethodPISA
2
C: Bloom syndrome protein
D: Bloom syndrome protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,25715
Polymers12,7832
Non-polymers1,47413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-40 kcal/mol
Surface area6620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.082, 144.729, 96.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-507-

IOD

21A-602-

HOH

31A-631-

HOH

41A-636-

HOH

51C-617-

HOH

61C-631-

HOH

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Components

#1: Protein
Bloom syndrome protein / / DNA helicase / RecQ-like type 2 / RecQ2 / RecQ protein-like 3


Mass: 6391.555 Da / Num. of mol.: 4 / Fragment: UNP residues 362-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM, RECQ2, RECQL3 / Plasmid: pET15b-sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54132, DNA helicase
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl 0.1M pH8.5 PEG 1500 26% Glycerol 16%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.16→27.84 Å / Num. obs: 12345 / % possible obs: 92.57 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.73 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08213 / Net I/σ(I): 19.63
Reflection shellResolution: 2.16→2.237 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.1837 / Mean I/σ(I) obs: 7.06 / CC1/2: 0.988 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LUS

5lus


Resolution: 2.16→27.84 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 30.31
RfactorNum. reflection% reflectionSelection details
Rfree0.2969 580 4.7 %5%
Rwork0.2186 ---
obs0.2223 12342 91.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.16→27.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 23 134 1830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021681
X-RAY DIFFRACTIONf_angle_d0.3972252
X-RAY DIFFRACTIONf_dihedral_angle_d10.8631086
X-RAY DIFFRACTIONf_chiral_restr0.034276
X-RAY DIFFRACTIONf_plane_restr0.002287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.2580.33651140.25412527X-RAY DIFFRACTION84
2.258-2.3770.35121420.24762866X-RAY DIFFRACTION99
2.377-2.52590.28931380.22742906X-RAY DIFFRACTION98
2.5259-2.72080.31571260.23482348X-RAY DIFFRACTION80
2.7208-2.99430.31541540.23682917X-RAY DIFFRACTION99
2.9943-3.4270.31411500.21282835X-RAY DIFFRACTION97
3.427-4.31540.27981010.17152370X-RAY DIFFRACTION85
4.3154-27.840.25411390.22572825X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.02070.0663-0.06380.3208-0.1360.43770.07250.01860.18780.0713-0.01960.2147-0.0266-0.05690.18110.10420.02540.00340.1649-0.02040.2059-16.621-2.2125-6.445
20.2887-0.09660.05070.0383-0.03330.10760.06790.1982-0.2166-0.0588-0.001-0.07310.09880.0083-0.18070.03320.080.06110.2607-0.13840.578-2.5296-7.6136-15.6634
30.6285-0.1001-0.15950.33610.15390.47920.06120.26890.2494-0.05070.0753-0.1339-0.1834-0.05490.5020.160.03250.0260.22690.04720.2637-10.50342.6194-14.4395
40.1668-0.0428-0.09280.19290.3270.5580.07770.0996-0.43330.1554-0.0577-0.01570.2978-0.1629-0.20830.1301-0.0023-0.02490.1653-0.02330.3735-17.9872-14.6393-11.0247
50.69580.27560.11510.10530.03940.0138-0.09350.0497-0.1823-0.05810.1760.0389-0.03260.05810.12740.38480.00730.08860.15860.03580.2057-19.832921.6161-11.3075
62.51140.40810.50140.30050.01730.148-0.35330.05830.57460.1079-0.0264-0.0999-0.1533-0.0033-0.31650.330.0028-0.06530.22490.03350.1719-14.865639.1459-17.5846
70.05020.02590.00820.0629-0.10260.2232-0.0507-0.0343-0.02040.03250.0085-0.05270.02170.053-0.05640.61280.1299-0.06110.21410.03390.0595-11.118928.753-11.501
80.0718-0.00340.05190.00210.00940.1393-0.086-0.0618-0.03740.17970.02610.0968-0.107-0.014-0.0280.63920.02220.19880.3187-0.04490.4997-29.447640.528-10.5676
90.05470.0492-0.05470.0705-0.02150.0789-0.0408-0.02550.00480.07580.1080.09680.0983-0.05180.1590.5460.07520.18690.16560.11830.1496-26.687927.9786-6.9344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 364 through 385 )
2X-RAY DIFFRACTION2chain 'A' and (resid 386 through 414 )
3X-RAY DIFFRACTION3chain 'B' and (resid 362 through 385 )
4X-RAY DIFFRACTION4chain 'B' and (resid 386 through 413 )
5X-RAY DIFFRACTION5chain 'C' and (resid 362 through 385 )
6X-RAY DIFFRACTION6chain 'C' and (resid 386 through 413 )
7X-RAY DIFFRACTION7chain 'D' and (resid 365 through 385 )
8X-RAY DIFFRACTION8chain 'D' and (resid 386 through 396 )
9X-RAY DIFFRACTION9chain 'D' and (resid 397 through 412 )

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