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- PDB-7vbg: N Terminal Domain of PRC1 -

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Basic information

Entry
Database: PDB / ID: 7vbg
TitleN Terminal Domain of PRC1
ComponentsProtein regulator of cytokinesis 1
KeywordsCELL CYCLE / regulator
Function / homology
Function and homology information


contractile ring / mitotic spindle midzone / mitotic spindle elongation / mitotic spindle midzone assembly / RHO GTPases activate CIT / kinesin binding / intercellular bridge / regulation of cytokinesis / spindle microtubule / microtubule cytoskeleton organization ...contractile ring / mitotic spindle midzone / mitotic spindle elongation / mitotic spindle midzone assembly / RHO GTPases activate CIT / kinesin binding / intercellular bridge / regulation of cytokinesis / spindle microtubule / microtubule cytoskeleton organization / spindle / spindle pole / chromosome / microtubule cytoskeleton / midbody / microtubule binding / cell division / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Microtubule-associated protein, MAP65/Ase1/PRC1 / Microtubule associated protein (MAP65/ASE1 family)
Similarity search - Domain/homology
Protein regulator of cytokinesis 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsTan, F. / Xia, B.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, China)2012CB910703 China
CitationJournal: To Be Published
Title: N Terminal Domain of PRC1
Authors: Tan, F. / Xia, B.
History
DepositionAug 31, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1May 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

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Assembly

Deposited unit
A: Protein regulator of cytokinesis 1
B: Protein regulator of cytokinesis 1


Theoretical massNumber of molelcules
Total (without water)16,0972
Polymers16,0972
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, This experiment proves that the unit is homodimeric based on measured molecular mass., cross-linking, molecular weight of the protein proves itself as a homodimer., gel filtration, ...Evidence: SAXS, This experiment proves that the unit is homodimeric based on measured molecular mass., cross-linking, molecular weight of the protein proves itself as a homodimer., gel filtration, molecular weight of the protein proves itself as a homodimer., immunoprecipitation, one monomer of the protein coimmunoprecipitate with itself proves it to be a homodimer.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area4990 Å2
ΔGint-48 kcal/mol
Surface area7960 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Protein regulator of cytokinesis 1


Mass: 8048.385 Da / Num. of mol.: 2 / Fragment: N Terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O43663

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic23D 1H-15N NOESY
123isotropic23D 1H-13C NOESY
133isotropic23D 1H-13C NOESY aliphatic
143isotropic23D 1H-13C NOESY aromatic
153isotropic23D 1H-13C Isotope Filtered CNOESY
162isotropic22D 1H-15N HSQC
172isotropic22D 1H-15N HMQC
181isotropic23D HN(CA)CB
191isotropic23D CBCA(CO)NH
1101isotropic23D HNCA
1171isotropic23D HNCO
1111isotropic23D HN(CO)CA
1121isotropic23D HBHA(CO)NH
1131isotropic23D (H)CCH-TOCSY
1141isotropic23D (H)CCH-TOCSY
1151isotropic23D (H)CCH-COSY
1161isotropic23D (H)CCH-COSY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mM [U-13C; U-15N] Protein, 50 mM NA sodium phosphate, 150 mM NA sodium chloride, 20 mM NA DTT, 0.1 mM NA DSS, 90% H2O/10% D2OSlightly higher PH is to keep the protein from being aggregatory13C_15N sample90% H2O/10% D2O
solution21 mM [U-13C; U-15N] Protein, 50 mM NA sodium phosphate, 150 mM NA sodium chloride, 20 mM NA DTT, 0.1 mM NA DSS, 90% H2O/10% D2OSlightly higher PH is to keep the protein from being aggregatory15N sample90% H2O/10% D2O
solution31 mM [U-13C; U-15N] Protein, 50 mM NA sodium phosphate, 150 mM NA sodium chloride, 20 mM NA DTT, 0.1 mM NA DSS, 90% H2O/10% D2OSlightly higher PH is to keep the protein from being aggregatory13C sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMProtein[U-13C; U-15N]1
50 mMsodium phosphateNA1
150 mMsodium chlorideNA1
20 mMDTTNA1
0.1 mMDSSNA1
1 mMProtein[U-13C; U-15N]2
50 mMsodium phosphateNA2
150 mMsodium chlorideNA2
20 mMDTTNA2
0.1 mMDSSNA2
1 mMProtein[U-13C; U-15N]3
50 mMsodium phosphateNA3
150 mMsodium chlorideNA3
20 mMDTTNA3
0.1 mMDSSNA3
Sample conditions

Details: A slightly higher PH is to keep the protein from being aggregatory / Ionic strength: 150 mM / Ionic strength err: 1 / pH: 7.4 / PH err: 0.1 / Pressure: 101325 Pa / Pressure err: 0.1 / Temperature err: 0.2

Conditions-IDLabelTemperature (K)
1condition_1298 K
2condition_2295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificpeak picking
AmberCase, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 4
Details: the structure is based on a total of 3717 distance restraints, 256 dihedral angle restraints and 7 hydrogen bonding restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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