[English] 日本語
Yorodumi
- PDB-2le8: The protein complex for DNA replication -

+
Open data


ID or keywords:

Loading...

-
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 DNA replication origin binding / Switching of origins to a post-replicative state / regulation of nuclear cell cycle DNA replication / Unwinding of DNA / negative regulation of DNA-templated DNA replication / mitotic DNA replication / CMG complex ...DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / regulation of DNA replication origin binding / Switching of origins to a post-replicative state / regulation of nuclear cell cycle DNA replication / Unwinding of DNA / negative regulation of DNA-templated DNA replication / mitotic DNA replication / CMG complex / DNA replication checkpoint signaling / attachment of mitotic spindle microtubules to kinetochore / MCM complex / double-strand break repair via break-induced replication / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / 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 / single-stranded DNA binding / mitotic cell cycle / 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 / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
Water0
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

-
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

-
Experimental details

-
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

-
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

-
NMR measurement

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more