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- PDB-2le8: The protein complex for DNA replication -

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Basic information

Entry
Database: PDB / ID: 2le8
TitleThe protein complex for DNA replication
Components
  • DNA replication factor Cdt1
  • DNA replication licensing factor MCM6
KeywordsREPLICATION / DNA replication
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / Unwinding of DNA / mitotic DNA replication / CMG complex / attachment of mitotic spindle microtubules to kinetochore ...DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / regulation of nuclear cell cycle DNA replication / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / Unwinding of DNA / mitotic DNA replication / CMG complex / attachment of mitotic spindle microtubules to kinetochore / DNA replication checkpoint signaling / MCM complex / double-strand break repair via break-induced replication / regulation of DNA-templated DNA replication initiation / positive regulation of chromatin binding / DNA unwinding involved in DNA replication / G1/S-Specific Transcription / negative regulation of cell cycle / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / DNA polymerase binding / DNA helicase activity / positive regulation of DNA replication / Assembly of the pre-replicative complex / kinetochore / Orc1 removal from chromatin / mitotic cell cycle / single-stranded DNA binding / DNA helicase / DNA replication / chromosome, telomeric region / nuclear body / cell division / chromatin binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #870 / CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / DNA replication licensing factor Mcm6 / Mcm6, C-terminal winged-helix domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #870 / CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / DNA replication licensing factor Mcm6 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Winged helix DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
DNA replication licensing factor MCM6 / DNA replication factor Cdt1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model 1
AuthorsLiu, C. / Wei, Z. / Zhu, G.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural insights into the Cdt1-mediated MCM2-7 chromatin loading
Authors: Liu, C. / Wu, R. / Zhou, B. / Wang, J. / Wei, Z. / Tye, B.K. / Liang, C. / Zhu, G.
History
DepositionJun 14, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 19, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA replication licensing factor MCM6
B: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)16,6662
Polymers16,6662
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)19 / 200structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA replication licensing factor MCM6 / p105MCM


Mass: 13303.877 Da / Num. of mol.: 1 / Fragment: UNP residues 708-821 / Mutation: C18S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14566
#2: Protein/peptide DNA replication factor Cdt1 / Double parked homolog / DUP


Mass: 3361.915 Da / Num. of mol.: 1 / Fragment: UNP residues 413-440
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDT1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H211

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D C(CO)NH
1613D H(CCO)NH
1723D (H)CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-15N NOESY
110113C/15N filtered-C13 edited NOE
11112D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
125 mM MES-1, 300 mM sodium chloride-2, 1 % glycerol-3, 0.8 mM [U-100% 13C; U-100% 15N] entity_2-4, 1 mM entity_1-5, 90% H2O/10% D2O90% H2O/10% D2O
225 mM [U-100% 15N] MES-6, 300 mM sodium chloride-7, 1 % glycerol-8, 0.8 mM [U-100% 13C; U-100% 15N] entity_1-9, 1.0 mM entity_2-10, 90% H2O/10% D2O90% H2O/10% D2O
325 mM MES-11, 300 mM sodium chloride-12, 1 % glycerol-13, 0.8 mM [U-100% 13C; U-100% 15N] entity_1-14, 1.0 mM entity_2-15, 100% D2O100% D2O
425 mM MES-16, 300 mM sodium chloride-17, 1 % glycerol-18, 0.8 mM [U-100% 13C; U-100% 15N] entity_2-19, 1.0 mM entity_1-20, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
25 mMMES-11
300 mMsodium chloride-21
1 %glycerol-31
0.8 mMentity_2-4[U-100% 13C; U-100% 15N]1
1 mMentity_1-51
25 mMMES-6[U-100% 15N]2
300 mMsodium chloride-72
1 %glycerol-82
0.8 mMentity_1-9[U-100% 13C; U-100% 15N]2
1.0 mMentity_2-102
25 mMMES-113
300 mMsodium chloride-123
1 %glycerol-133
0.8 mMentity_1-14[U-100% 13C; U-100% 15N]3
1.0 mMentity_2-153
25 mMMES-164
300 mMsodium chloride-174
1 %glycerol-184
0.8 mMentity_2-19[U-100% 13C; U-100% 15N]4
1.0 mMentity_1-204
Sample conditionsIonic strength: 3 / pH: 6.5 / Pressure: ambient / Temperature: 310 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameDeveloperClassification
VNMRVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
HADDOCK1.3Alexandre Bonvinrefinement
ProcheckNMRLaskowski and MacArthurgeometry optimization
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 19 / Representative conformer: 1

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