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- PDB-7wu8: Crystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1 -

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Basic information

Entry
Database: PDB / ID: 7wu8
TitleCrystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1
ComponentsRegulator of telomere elongation helicase 1
KeywordsPROTEIN BINDING / RTEL1 / Harmonin homology domain 2 / Protein-protein interaction / Protein-DNA interaction
Function / homology
Function and homology information


DNA strand displacement / telomeric loop disassembly / negative regulation of telomere maintenance in response to DNA damage / positive regulation of telomeric loop disassembly / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / Cytosolic iron-sulfur cluster assembly / positive regulation of telomere maintenance via telomere lengthening / negative regulation of t-circle formation / mitotic telomere maintenance via semi-conservative replication / negative regulation of DNA recombination ...DNA strand displacement / telomeric loop disassembly / negative regulation of telomere maintenance in response to DNA damage / positive regulation of telomeric loop disassembly / Isomerases; Isomerases altering macromolecular conformation; Enzymes altering nucleic acid conformation / Cytosolic iron-sulfur cluster assembly / positive regulation of telomere maintenance via telomere lengthening / negative regulation of t-circle formation / mitotic telomere maintenance via semi-conservative replication / negative regulation of DNA recombination / positive regulation of telomere capping / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / regulation of double-strand break repair via homologous recombination / positive regulation of telomere maintenance / replication fork processing / telomere maintenance in response to DNA damage / Telomere Extension By Telomerase / DNA polymerase binding / telomere maintenance / DNA helicase activity / 4 iron, 4 sulfur cluster binding / nuclear membrane / chromosome, telomeric region / nuclear speck / DNA repair / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus
Similarity search - Function
Regulator of telomere elongation helicase 1 / : / RTEL1 helicase, ARCH domain / RTEL1, HHD domain / Paired amphipathic helix 2 (pah2 repeat) - #20 / Paired amphipathic helix 2 (pah2 repeat) / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 ...Regulator of telomere elongation helicase 1 / : / RTEL1 helicase, ARCH domain / RTEL1, HHD domain / Paired amphipathic helix 2 (pah2 repeat) - #20 / Paired amphipathic helix 2 (pah2 repeat) / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
Regulator of telomere elongation helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsKumar, N. / Rothweiler, U. / Singh, M.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR15829/BRB/10/1469/2015 India
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides insights into its recruitment to DNA repair sites.
Authors: Kumar, N. / Taneja, A. / Ghosh, M. / Rothweiler, U. / Sundaresan, N.R. / Singh, M.
History
DepositionFeb 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Regulator of telomere elongation helicase 1
B: Regulator of telomere elongation helicase 1
C: Regulator of telomere elongation helicase 1
D: Regulator of telomere elongation helicase 1
E: Regulator of telomere elongation helicase 1
F: Regulator of telomere elongation helicase 1
G: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)74,4597
Polymers74,4597
Non-polymers00
Water13,223734
1
A: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)10,6371
Polymers10,6371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.640, 60.960, 79.710
Angle α, β, γ (deg.)90.000, 95.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Regulator of telomere elongation helicase 1 / Novel helicase-like


Mass: 10637.021 Da / Num. of mol.: 7 / Fragment: HHD2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RTEL1, C20orf41, KIAA1088, NHL / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZ71, DNA helicase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.14 Å3/Da / Density % sol: 42.4 % / Description: Needle shaped crystal
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 20mM Tris pH7.4, 250mM NaCl, 5% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2020 / Details: Toroidal mirror
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.599→48.336 Å / Num. obs: 80150 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.47 % / Biso Wilson estimate: 31.52 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.053 / Χ2: 0.98 / Net I/σ(I): 13.48
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID% possible all
1.599-1.61.73126980.8020.64195.3
1.6-1.72.79120110.9150.425196.1
1.7-1.814.86112610.970.241196.4
1.81-1.969.18104200.9890.133197
1.96-2.1414.3694750.9950.086197.3
2.14-2.420.4184000.9970.059197.5
2.4-2.7730.371500.9990.041197.9
2.77-3.3939.8255880.9990.0311
3.39-4.7840.7831470.9990.031

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSFebruary 5, 2021data scaling
PDB_EXTRACT3.27data extraction
XDSFebruary 5, 2021data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF-Q9NZ71-F1

Resolution: 1.599→48.156 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.177 / Average fsc free: 0.9054 / Average fsc work: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2012 2100 2.62 %
Rwork0.1765 78046 -
all0.177 --
obs-80146 96.76 %
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: 27.133 Å2
Baniso -1Baniso -2Baniso -3
1-0.174 Å2-0 Å21.443 Å2
2--0.144 Å2-0 Å2
3----0.592 Å2
Refinement stepCycle: LAST / Resolution: 1.599→48.156 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 0 735 5123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134483
X-RAY DIFFRACTIONr_bond_other_d0.0360.0174203
X-RAY DIFFRACTIONr_angle_refined_deg1.8951.6436078
X-RAY DIFFRACTIONr_angle_other_deg2.341.5839689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5765567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69520.478230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97815724
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8231537
X-RAY DIFFRACTIONr_chiral_restr0.1080.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025039
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02984
X-RAY DIFFRACTIONr_nbd_refined0.2460.21064
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.23724
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22349
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.22056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2434
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1020.27
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1580.222
X-RAY DIFFRACTIONr_nbd_other0.2010.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1610.249
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0760.21
X-RAY DIFFRACTIONr_mcbond_it2.6572.5852286
X-RAY DIFFRACTIONr_mcbond_other2.6492.5832285
X-RAY DIFFRACTIONr_mcangle_it3.7563.8552847
X-RAY DIFFRACTIONr_mcangle_other3.7583.8562848
X-RAY DIFFRACTIONr_scbond_it3.8483.032197
X-RAY DIFFRACTIONr_scbond_other3.8473.0322198
X-RAY DIFFRACTIONr_scangle_it5.8724.3743231
X-RAY DIFFRACTIONr_scangle_other5.8714.3763232
X-RAY DIFFRACTIONr_lrange_it7.21433.4725409
X-RAY DIFFRACTIONr_lrange_other6.99232.285174
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
1.599-1.6410.3171500.27955920.2860790.7450.76694.45630.268
1.641-1.6860.3111490.26255440.26359530.7920.82195.63250.248
1.686-1.7350.2861450.24353710.24457470.8470.85295.98050.226
1.735-1.7880.261420.22652680.22756260.8870.88596.16070.206
1.788-1.8460.2571370.21650950.21754250.8780.90196.44240.193
1.846-1.9110.2661330.20149400.20352550.9060.91796.53660.178
1.911-1.9830.221280.18847700.18950840.9390.93896.34150.168
1.983-2.0640.1881240.17546100.17548850.9440.94796.90890.158
2.064-2.1560.1951190.16744400.16846880.9440.95597.24830.155
2.156-2.2610.1891160.1642870.16145290.9570.95597.21790.147
2.261-2.3830.2091080.15540210.15642390.9430.95897.4050.144
2.383-2.5270.1931040.15838670.15940920.9570.96397.0430.151
2.527-2.7010.185970.15836100.15937900.9530.96297.810.155
2.701-2.9160.201910.16933820.16935450.9530.95797.9690.167
2.916-3.1930.186850.16531480.16632990.9520.96397.99940.17
3.193-3.5680.205750.17328100.17429570.9480.95797.56510.182
3.568-4.1170.157680.14925190.14926370.9650.97298.10390.165
4.117-5.0330.147580.16421540.16322480.9740.97198.39860.187
5.033-7.0790.261440.23616510.23717300.9280.94697.97690.265
7.079-48.1560.187270.1789680.17810190.9630.96297.64480.23

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