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

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Basic information

Entry
Database: PDB / ID: 5lup
TitleStructures of DHBN domain of human BLM helicase
Components(BLM protein) x 2
KeywordsSTRUCTURAL PROTEIN / helicase dimerization alpha-helix motif
Function / homology
Function and homology information


RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / 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 / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin ...RecQ family helicase-topoisomerase III complex / telomeric G-quadruplex DNA binding / 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 / t-circle formation / telomeric D-loop disassembly / cellular response to camptothecin / DNA geometric change / Y-form DNA binding / negative regulation of cell division / cellular response to hydroxyurea / G-quadruplex DNA binding / lateral element / negative regulation of DNA recombination / bubble DNA binding / DNA double-strand break processing / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / Impaired BRCA2 binding to PALB2 / Processive synthesis on the C-strand of the telomere / regulation of cyclin-dependent protein serine/threonine kinase activity / Homologous DNA Pairing and Strand Exchange / 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 / 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 3'-5' helicase / HDR through Single Strand Annealing (SSA) / nuclear chromosome / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / protein complex oligomerization / replication fork processing / Presynaptic phase of homologous DNA pairing and strand exchange / ATP-dependent activity, acting on DNA / response to X-ray / SUMOylation of DNA damage response and repair proteins / DNA helicase activity / four-way junction DNA binding / telomere maintenance / replication fork / cellular response to ionizing radiation / isomerase activity / helicase activity / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / protein homooligomerization / Meiotic recombination / HDR through Homologous Recombination (HRR) / nuclear matrix / p53 binding / single-stranded DNA binding / chromosome / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / DNA replication / DNA repair / DNA damage response / positive regulation of DNA-templated transcription / nucleolus / protein homodimerization activity / protein-containing complex / ATP hydrolysis activity / 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 / Helicase and RNase D C-terminal ...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 / Helicase and RNase D C-terminal / HRDC domain / HRDC domain / HRDC domain profile. / ATP-dependent DNA helicase RecQ, zinc-binding domain / RecQ zinc-binding / DNA helicase, ATP-dependent, RecQ type / 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 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / PHOSPHATE ION / RecQ-like DNA helicase BLM / BLM protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.032 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
DepositionSep 9, 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
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: BLM protein
B: BLM protein
C: BLM protein
D: BLM protein
E: BLM protein
F: BLM protein
G: BLM protein
H: BLM protein
I: BLM protein
J: BLM protein
K: BLM protein
L: BLM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,96716
Polymers76,69912
Non-polymers2684
Water7,999444
1
A: BLM protein
B: BLM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9174
Polymers12,7832
Non-polymers1342
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-35 kcal/mol
Surface area6730 Å2
MethodPISA
2
C: BLM protein
D: BLM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8223
Polymers12,7832
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-34 kcal/mol
Surface area6870 Å2
MethodPISA
3
E: BLM protein
F: BLM protein


Theoretical massNumber of molelcules
Total (without water)12,7832
Polymers12,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-34 kcal/mol
Surface area6730 Å2
MethodPISA
4
G: BLM protein
H: BLM protein


Theoretical massNumber of molelcules
Total (without water)12,7832
Polymers12,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-32 kcal/mol
Surface area6790 Å2
MethodPISA
5
I: BLM protein
J: BLM protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8783
Polymers12,7832
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-37 kcal/mol
Surface area6670 Å2
MethodPISA
6
K: BLM protein
L: BLM protein


Theoretical massNumber of molelcules
Total (without water)12,7832
Polymers12,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-34 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.795, 132.795, 64.984
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein
BLM protein


Mass: 6391.555 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q3B7X0, UniProt: P54132*PLUS
#2: Protein BLM protein


Mass: 6391.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BLM / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q3B7X0, UniProt: P54132*PLUS
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Tris-HCl 0.1M PH8.5 PEG1500 2% Glycerol 16%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 1.7 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.032→43.47 Å / Num. obs: 41409 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07402 / Net I/σ(I): 18.34
Reflection shellHighest resolution: 2.105 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5345 / Mean I/σ(I) obs: 1.84 / CC1/2: 0.767 / % possible all: 87

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.032→43.47 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 29.18
RfactorNum. reflection% reflectionSelection details
Rfree0.2626 1985 4.8 %5%
Rwork0.2103 ---
obs0.2129 41384 97.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.032→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5087 0 12 444 5543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075119
X-RAY DIFFRACTIONf_angle_d0.9526857
X-RAY DIFFRACTIONf_dihedral_angle_d15.8262095
X-RAY DIFFRACTIONf_chiral_restr0.037836
X-RAY DIFFRACTIONf_plane_restr0.003874
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0324-2.08330.34481140.31332455X-RAY DIFFRACTION86
2.0833-2.13960.34761230.26752607X-RAY DIFFRACTION91
2.1396-2.20250.3221480.24332724X-RAY DIFFRACTION96
2.2025-2.27360.321450.23282844X-RAY DIFFRACTION99
2.2736-2.35490.26621320.22222870X-RAY DIFFRACTION100
2.3549-2.44920.29211510.22292846X-RAY DIFFRACTION100
2.4492-2.56060.31091420.21362878X-RAY DIFFRACTION100
2.5606-2.69560.24741480.22052860X-RAY DIFFRACTION100
2.6956-2.86450.30011440.2272846X-RAY DIFFRACTION100
2.8645-3.08560.28991480.22712876X-RAY DIFFRACTION100
3.0856-3.3960.28971410.21572871X-RAY DIFFRACTION100
3.396-3.88730.23381610.18982871X-RAY DIFFRACTION100
3.8873-4.89670.23521410.17252905X-RAY DIFFRACTION100
4.8967-46.45440.20961470.20492946X-RAY DIFFRACTION99
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)
10.4212-0.2355-0.64140.09380.15480.39560.1407-0.09440.0119-0.3014-0.3755-0.2509-0.0940.0716-0.00550.2051-0.0113-0.03050.1426-0.05080.1218-3.717231.48814.2334
20.03610.093-0.09020.308-0.4050.417-0.06850.1012-0.18160.0449-0.2409-0.25230.13390.1876-0.0230.14480.0008-0.04270.17170.00430.2871-3.02359.393415.3416
30.3622-0.0289-0.07690.3332-0.11660.1423-0.17730.427-0.09110.18970.02750.32490.17670.7188-0.02960.2069-0.0402-0.01720.2231-0.00870.14776.498919.046317.2484
40.4122-0.26050.13531.0642-0.53280.6635-0.21790.00030.1551-0.1232-0.10380.0859-0.33710.1173-0.04390.1998-0.0581-0.0160.20710.03140.16996.474927.29611.9398
5-0.05950.3723-0.38440.796-0.14531.2278-0.22470.0502-0.0981-0.08930.29150.1966-0.1821-0.49090.02680.13590.0195-0.04510.2128-0.0340.1951-12.000221.302410.844
60.4060.1171-0.35260.75940.60670.6446-0.3034-0.32710.1160.28060.07610.1868-0.2352-0.2816-0.00950.17790.0663-0.00950.1902-0.01470.2665-3.733526.643837.1179
70.2763-0.33320.6511.097-1.06790.9175-0.15610.0923-0.13680.14950.0168-0.2250.12780.0623-0.05610.1507-0.0013-0.02540.1503-0.00060.191815.339622.958238.5554
80.78850.1666-0.39990.578-0.49150.46370.0403-0.0672-0.013-0.2694-0.0734-0.0488-0.45850.01920.00330.25250.0228-0.05280.1284-0.00090.14696.427532.285936.6761
90.4141-0.18920.48680.7581-0.12381.616-0.1671-0.1255-0.37040.00090.24370.2949-0.0535-0.3271-0.01770.1125-0.0132-0.00140.08070.02670.23811.358815.121332.0023
100.57180.5069-0.27120.57050.36050.2871-0.1091-0.0126-0.0161-0.5885-0.1990.3014-0.3194-0.1512-0.01130.289-0.00630.02420.17690.03840.16536.481244.448613.6767
110.44330.0441-0.01640.33950.30950.5210.1109-0.14480.68040.05780.00930.5133-0.0391-0.1508-0.00090.27880.00810.05350.20070.01480.37511.361761.726818.4171
120.53610.24230.84380.50560.57071.1308-0.45960.460.355-0.46250.21330.28280.4004-0.3268-00.2646-0.04050.04990.2749-0.03190.2432-3.29350.392612.8915
130.0342-0.0851-0.01852.8893-0.63290.1492-0.25130.4866-0.57290.424-0.2116-0.97110.22920.0324-0.15860.3881-0.12030.09820.374-0.05590.331617.222361.179515.0575
140.4120.2915-0.33860.4068-0.18690.1081-0.15370.19290.0421-0.668-0.1854-0.4364-0.340.0986-0.00750.3047-0.03630.04280.23850.02040.227213.984649.06859.5218
150.7795-0.14180.06950.0686-0.2180.3805-0.0333-0.0009-0.11040.282-0.05510.1644-0.003-0.2928-0.02810.2428-0.03810.02440.1715-0.02190.2299-3.50844.243637.0065
160.63770.5652-0.41620.5644-0.01960.5133-0.199-0.02050.26980.27420.0407-0.00250.05910.2709-00.29530.0003-0.01440.2410.01150.25842.978561.22133.8332
170.2591-0.1774-0.37070.5095-0.7350.5841-0.0952-0.1544-0.12550.01840.01220.00970.23080.1222-00.27390.0107-0.00810.2242-0.03030.25956.533149.434938.3532
180.0424-0.02370.07850.0606-0.02290.0518-0.05050.0517-0.4109-0.2150.26480.417-0.26950.078500.25770.0661-0.00590.2738-0.04450.3452-12.805662.725738.3894
190.39430.2498-0.12230.44460.06030.1662-0.0656-0.0286-0.07750.0129-0.00070.56380.2633-0.3699-0.00110.2516-0.01080.05760.2437-0.06420.2478-11.333149.827740.7154
200.63510.15170.03240.31710.3620.44070.04340.1875-0.30380.1882-0.3757-0.0117-0.07420.1944-0.00160.29840.00450.04770.197-0.00440.323420.906461.302434.1048
210.4867-0.46340.27150.5866-0.75560.7608-0.02720.10450.15430.398-0.16970.05450.05470.0826-00.3132-0.04240.01710.2772-0.00050.282627.32178.715833.8743
220.29880.3602-0.06030.9956-0.05520.0228-0.09730.1009-0.09570.2462-0.14710.06360.25480.278200.29770.0328-0.00690.42410.05560.270430.52366.422535.9851
230.54780.0695-0.49820.59950.66231.25990.06810.1054-0.00280.005-0.13360.6536-0.08130.062800.17120.0062-0.00770.237-0.00880.275313.384271.259939.5706
240.54950.5546-0.25670.4367-0.01760.2722-0.1409-0.17750.065-0.0214-0.30610.17070.427-0.4712-0.08660.4173-0.07580.04440.2727-0.02550.276-20.668458.613817.0304
250.5540.36180.1106-0.02780.08760.6543-0.07560.07170.5289-0.16570.09190.06290.0271-0.3985-0.00180.2341-0.0227-0.02380.3931-0.04490.2972-24.823376.297618.2529
260.2006-0.1233-0.02132.4777-0.1647-0.06530.0606-0.1973-0.0715-0.5786-0.0567-0.0028-0.0296-0.7797-0.13770.1735-0.099-0.12380.5911-0.04060.214-29.450964.959514.605
271.2242-0.548-0.67360.35770.60310.4558-0.1644-0.15280.3569-0.1320.0015-0.080.48280.1862-00.4168-0.02720.01430.3286-0.03980.2662-11.958566.570512.0013
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 53 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 52 )
6X-RAY DIFFRACTION6chain 'C' and (resid 1 through 25 )
7X-RAY DIFFRACTION7chain 'C' and (resid 26 through 54 )
8X-RAY DIFFRACTION8chain 'D' and (resid 2 through 25 )
9X-RAY DIFFRACTION9chain 'D' and (resid 26 through 54 )
10X-RAY DIFFRACTION10chain 'E' and (resid 2 through 25 )
11X-RAY DIFFRACTION11chain 'E' and (resid 26 through 54 )
12X-RAY DIFFRACTION12chain 'F' and (resid 2 through 25 )
13X-RAY DIFFRACTION13chain 'F' and (resid 26 through 38 )
14X-RAY DIFFRACTION14chain 'F' and (resid 39 through 53 )
15X-RAY DIFFRACTION15chain 'G' and (resid 2 through 25 )
16X-RAY DIFFRACTION16chain 'G' and (resid 26 through 53 )
17X-RAY DIFFRACTION17chain 'H' and (resid 2 through 25 )
18X-RAY DIFFRACTION18chain 'H' and (resid 26 through 36 )
19X-RAY DIFFRACTION19chain 'H' and (resid 37 through 53 )
20X-RAY DIFFRACTION20chain 'I' and (resid 3 through 25 )
21X-RAY DIFFRACTION21chain 'I' and (resid 26 through 53 )
22X-RAY DIFFRACTION22chain 'J' and (resid 4 through 25 )
23X-RAY DIFFRACTION23chain 'J' and (resid 26 through 52 )
24X-RAY DIFFRACTION24chain 'K' and (resid 4 through 25 )
25X-RAY DIFFRACTION25chain 'K' and (resid 26 through 53 )
26X-RAY DIFFRACTION26chain 'L' and (resid 4 through 25 )
27X-RAY DIFFRACTION27chain 'L' and (resid 26 through 53 )

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