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- PDB-8ya8: The crystal structure of human Rtel1 HHD2 domain -

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Basic information

Entry
Database: PDB / ID: 8ya8
TitleThe crystal structure of human Rtel1 HHD2 domain
ComponentsRegulator of telomere elongation helicase 1
KeywordsHYDROLASE / Regulator of telomere elongation helicase 1 / DNA BINDING PROTEIN
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 / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like ...Regulator of telomere elongation helicase 1 / : / RTEL1 helicase, ARCH domain / RTEL1, HHD domain / 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. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Regulator of telomere elongation helicase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChun, I.S. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biodesign / Year: 2024
Title: Crystal structure of the HHD2 domain in human RTEL1
Authors: Chun, I. / Jung, E. / Kim, W.J. / Kim, M.S.
History
DepositionFeb 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _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)68,1607
Polymers68,1607
Non-polymers00
Water86548
1
A: Regulator of telomere elongation helicase 1


Theoretical massNumber of molelcules
Total (without water)9,7371
Polymers9,7371
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)9,7371
Polymers9,7371
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)9,7371
Polymers9,7371
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)9,7371
Polymers9,7371
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)9,7371
Polymers9,7371
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)9,7371
Polymers9,7371
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)9,7371
Polymers9,7371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.052, 61.958, 79.953
Angle α, β, γ (deg.)90.00, 95.14, 90.00
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: 9737.107 Da / Num. of mol.: 7 / Fragment: HHD2 domain
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.: 48 / 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: 2.39 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2 M Potassium sulfate, 20% (v/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. obs: 14421 / % possible obs: 94.3 % / Redundancy: 3.8 % / CC1/2: 0.999 / Net I/σ(I): 8.09
Reflection shellResolution: 2.85→2.95 Å / Mean I/σ(I) obs: 1.59 / Num. unique obs: 1393 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→48.9 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2684 720 5.01 %
Rwork0.2391 --
obs0.2406 14378 94.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4317 0 0 48 4365
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054401
X-RAY DIFFRACTIONf_angle_d0.8835962
X-RAY DIFFRACTIONf_dihedral_angle_d12.9721578
X-RAY DIFFRACTIONf_chiral_restr0.058696
X-RAY DIFFRACTIONf_plane_restr0.007767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-3.070.37381400.3332670X-RAY DIFFRACTION93
3.07-3.370.33311410.29592682X-RAY DIFFRACTION93
3.38-3.860.31581450.25312733X-RAY DIFFRACTION94
3.86-4.870.27591450.21122768X-RAY DIFFRACTION96
4.87-48.90.19261490.20672805X-RAY DIFFRACTION94

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