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- PDB-6kvg: The solution structure of human Orc6 -

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Basic information

Entry
Database: PDB / ID: 6kvg
TitleThe solution structure of human Orc6
ComponentsOrigin recognition complex subunit 6
KeywordsDNA BINDING PROTEIN / Orc6 / DNA
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / fibrillar center ...CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / fibrillar center / Orc1 removal from chromatin / DNA binding / nucleoplasm / membrane / nucleus / cytosol
Similarity search - Function
Origin recognition complex, subunit 6, metazoa/plant / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6)
Similarity search - Domain/homology
Origin recognition complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLiu, C. / Xu, N. / You, Y. / Zhu, G.
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Structural basis of DNA replication origin recognition by human Orc6 protein binding with DNA.
Authors: Xu, N. / You, Y. / Liu, C. / Balasov, M. / Lun, L.T. / Geng, Y. / Fung, C.P. / Miao, H. / Tian, H. / Choy, T.T. / Shi, X. / Fan, Z. / Zhou, B. / Akhmetova, K. / Din, R.U. / Yang, H. / Hao, Q. ...Authors: Xu, N. / You, Y. / Liu, C. / Balasov, M. / Lun, L.T. / Geng, Y. / Fung, C.P. / Miao, H. / Tian, H. / Choy, T.T. / Shi, X. / Fan, Z. / Zhou, B. / Akhmetova, K. / Din, R.U. / Yang, H. / Hao, Q. / Qian, P. / Chesnokov, I. / Zhu, G.
History
DepositionSep 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 18, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Origin recognition complex subunit 6


Theoretical massNumber of molelcules
Total (without water)28,4471
Polymers28,4471
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18950 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Origin recognition complex subunit 6 /


Mass: 28447.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC6, ORC6L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5N6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-15N NOESY
121isotropic23D 1H-15N TOCSY
132isotropic13D HNCO
142isotropic13D HN(CA)CB
152isotropic13D CBCA(CO)NH
162isotropic23D H(CCO)NH
172isotropic23D C(CO)NH
183isotropic13D 1H-13C NOESY
193isotropic13D (H)CCH-COSY
1103isotropic33D (H)CCH-TOCSY
1111isotropic12D 1H-15N HSQC
1123isotropic12D 1H-13C HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.7 mM [U-99% 15N] human Orc6, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution20.7 mM [U-99% 13C; U-99% 15N] human Orc6, 90% H2O/10% D2O13C15N_sample90% H2O/10% D2O
solution30.7 mM [U-99% 13C] human Orc6, 100% D2O13C_sample100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMhuman Orc6[U-99% 15N]1
0.7 mMhuman Orc6[U-99% 13C; U-99% 15N]2
0.7 mMhuman Orc6[U-99% 13C]3
Sample conditionsIonic strength: 150 mM / Label: conditions_1 / pH: 6.5 / Pressure: ambient Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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