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- PDB-5w2l: Structure of a central domain of human Ctc1 -

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Basic information

Entry
Database: PDB / ID: 5w2l
TitleStructure of a central domain of human Ctc1
ComponentsCST complex subunit CTC1
KeywordsDNA BINDING PROTEIN / Telomere / CST complex / Ctc1
Function / homology
Function and homology information


CST complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / G-rich strand telomeric DNA binding / telomere capping / Polymerase switching on the C-strand of the telomere / telomeric repeat DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance / positive regulation of DNA replication ...CST complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / G-rich strand telomeric DNA binding / telomere capping / Polymerase switching on the C-strand of the telomere / telomeric repeat DNA binding / negative regulation of telomere maintenance via telomerase / telomere maintenance / positive regulation of DNA replication / single-stranded DNA binding / chromosome, telomeric region / nucleoplasm / nucleus
Similarity search - Function
CST complex subunit CTC1 / CST complex subunit CTC1-like / : / : / : / : / : / : / CST, telomere maintenance, complex subunit CTC1 N-terminal domain / CST, telomere maintenance, complex subunit CTC1 second domain ...CST complex subunit CTC1 / CST complex subunit CTC1-like / : / : / : / : / : / : / CST, telomere maintenance, complex subunit CTC1 N-terminal domain / CST, telomere maintenance, complex subunit CTC1 second domain / CST, telomere maintenance, complex subunit CTC1 third domain / CST, telomere maintenance, complex subunit CTC1 fourth domain / CST, telomere maintenance, complex subunit CTC1 fifth domain / CST, telomere maintenance, complex subunit CTC1 sixth domain / CST, telomere maintenance, complex subunit CTC1 C-terminal domain
Similarity search - Domain/homology
: / CST complex subunit CTC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsRice, C. / Skordalakes, E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 RO1 CA201312-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R01 GM088332-03 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural and functional analysis of an OB-fold in human Ctc1 implicated in telomere maintenance and bone marrow syndromes.
Authors: Shastrula, P.K. / Rice, C.T. / Wang, Z. / Lieberman, P.M. / Skordalakes, E.
History
DepositionJun 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 3, 2018Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CST complex subunit CTC1
B: CST complex subunit CTC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0798
Polymers36,8752
Non-polymers1,2046
Water2,648147
1
A: CST complex subunit CTC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0404
Polymers18,4381
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint-58 kcal/mol
Surface area7950 Å2
MethodPISA
2
B: CST complex subunit CTC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0404
Polymers18,4381
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-35 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.537, 50.776, 144.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CST complex subunit CTC1 / Telomerase binding protein / Conserved telomere maintenance component 1 / HBV DNAPTP1-transactivated protein B


Mass: 18437.748 Da / Num. of mol.: 2 / Fragment: UNP residues 716-880
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTC1, C17orf68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2NKJ3
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES, pH 6.0, 20% w/v PEG2000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.86→40 Å / Num. obs: 30216 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.79 / Rpim(I) all: 0.325 / Net I/σ(I): 25
Reflection shellResolution: 1.86→1.9 Å / Mean I/σ(I) obs: 4.9 / CC1/2: 0.79 / Rpim(I) all: 0.325

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→19.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.973 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24914 1549 5.1 %RANDOM
Rwork0.20947 ---
obs0.21153 28663 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--1.04 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: 1 / Resolution: 1.86→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2194 0 6 148 2348
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192257
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9693061
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.385273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45523.53599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29515363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0471514
X-RAY DIFFRACTIONr_chiral_restr0.0740.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221726
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3753.9781110
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9895.9311377
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5724.0941147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined12.63832.573362
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 114 -
Rwork0.26 2071 -
obs--99.95 %

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