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- PDB-6qja: Organizational principles of the NuMA-Dynein interaction interfac... -

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Basic information

Entry
Database: PDB / ID: 6qja
TitleOrganizational principles of the NuMA-Dynein interaction interface and implications for mitotic spindle functions
ComponentsNuclear mitotic apparatus protein 1
KeywordsSTRUCTURAL PROTEIN / hook domain / motor protein-associated
Function / homology
Function and homology information


anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle ...anastral spindle assembly / positive regulation of protein localization to spindle pole body / positive regulation of mitotic spindle elongation / cytoplasmic microtubule bundle / positive regulation of chromosome separation / Mitotic Prophase / positive regulation of chromosome segregation / microtubule minus-end / cortical microtubule / microtubule bundle / lateral cell cortex / cell cortex region / mitotic spindle astral microtubule / positive regulation of intracellular transport / regulation of metaphase plate congression / mitotic spindle midzone / positive regulation of hair follicle development / astral microtubule organization / positive regulation of spindle assembly / microtubule minus-end binding / microtubule plus-end / positive regulation of BMP signaling pathway / positive regulation of keratinocyte differentiation / spindle pole centrosome / microtubule bundle formation / microtubule plus-end binding / dynein complex binding / nucleus organization / mitotic spindle pole / establishment of mitotic spindle orientation / lateral plasma membrane / positive regulation of protein localization to cell cortex / regulation of mitotic spindle organization / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / tubulin binding / phosphatidylinositol binding / meiotic cell cycle / spindle microtubule / mitotic spindle / nuclear matrix / spindle pole / spindle / disordered domain specific binding / chromosome / cell cortex / microtubule binding / protein domain specific binding / cell division / centrosome / neuronal cell body / dendrite / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
: / : / NuMA N-terminal hook domain
Similarity search - Domain/homology
Nuclear mitotic apparatus protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.54 Å
AuthorsRenna, C. / Rizzelli, F. / Carminati, M. / Gaddoni, C. / Pirovano, L. / Cecatiello, V. / Pasqualato, S. / Mapelli, M.
Funding support Italy, 2items
OrganizationGrant numberCountry
Italian Association for Cancer ResearchIG 18629 Italy
Other governmentRF-2013-02357254 Italy
CitationJournal: Structure / Year: 2020
Title: Organizational Principles of the NuMA-Dynein Interaction Interface and Implications for Mitotic Spindle Functions.
Authors: Renna, C. / Rizzelli, F. / Carminati, M. / Gaddoni, C. / Pirovano, L. / Cecatiello, V. / Pasqualato, S. / Mapelli, M.
History
DepositionJan 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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.title / _citation.year
Revision 1.2May 6, 2020Group: Structure summary / Category: audit_author / struct / Item: _struct.title
Revision 1.3May 27, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear mitotic apparatus protein 1
B: Nuclear mitotic apparatus protein 1
C: Nuclear mitotic apparatus protein 1
D: Nuclear mitotic apparatus protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3377
Polymers71,2424
Non-polymers953
Water9,062503
1
A: Nuclear mitotic apparatus protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8462
Polymers17,8101
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)17,8101
Polymers17,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nuclear mitotic apparatus protein 1


Theoretical massNumber of molelcules
Total (without water)17,8101
Polymers17,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nuclear mitotic apparatus protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8703
Polymers17,8101
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.730, 112.850, 135.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYSAA1 - 1535 - 157
21METMETLYSLYSBB1 - 1535 - 157
12THRTHRGLNGLNAA2 - 1526 - 156
22THRTHRGLNGLNCC2 - 1526 - 156
13METMETGLNGLNAA1 - 1525 - 156
23METMETGLNGLNDD1 - 1525 - 156
14THRTHRGLNGLNBB2 - 1526 - 156
24THRTHRGLNGLNCC2 - 1526 - 156
15METMETLYSLYSBB1 - 1535 - 157
25METMETLYSLYSDD1 - 1535 - 157
16THRTHRGLNGLNCC2 - 1526 - 156
26THRTHRGLNGLNDD2 - 1526 - 156

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Nuclear mitotic apparatus protein 1 / Nuclear matrix protein-22 / NMP-22 / Nuclear mitotic apparatus protein / NuMA protein / SP-H antigen


Mass: 17810.469 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUMA1, NMP22, NUMA / Plasmid: pETM14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14980
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Bis-Tris Propane, 0.2 M Magnesium Chloride, 28 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→67.91 Å / Num. obs: 104874 / % possible obs: 100 % / Redundancy: 6.5 % / CC1/2: 1 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.015 / Rrim(I) all: 0.039 / Net I/σ(I): 22.9
Reflection shellResolution: 1.54→1.57 Å / Mean I/σ(I) obs: 1.3 / CC1/2: 0.539

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
xia2data reduction
xia2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.54→67.9 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.96 / SU B: 6.706 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.077
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2147 5242 5 %RANDOM
Rwork0.1695 ---
obs0.1717 99539 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 224.22 Å2 / Biso mean: 39.247 Å2 / Biso min: 16.13 Å2
Baniso -1Baniso -2Baniso -3
1--4.42 Å20 Å20 Å2
2--3.47 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 1.54→67.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 3 503 5229
Biso mean--30.99 47.48 -
Num. residues----602
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0144826
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174441
X-RAY DIFFRACTIONr_angle_refined_deg1.671.6376537
X-RAY DIFFRACTIONr_angle_other_deg1.1491.63410380
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4395603
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82623.991233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49415874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0311519
X-RAY DIFFRACTIONr_chiral_restr0.0910.2634
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02847
X-RAY DIFFRACTIONr_rigid_bond_restr9.35739267
X-RAY DIFFRACTIONr_sphericity_free42.5125317
X-RAY DIFFRACTIONr_sphericity_bonded41.46359368
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A42050.16
12B42050.16
21A41380.16
22C41380.16
31A42850.17
32D42850.17
41B40210.15
42C40210.15
51B42000.16
52D42000.16
61C40880.17
62D40880.17
LS refinement shellResolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 388 -
Rwork0.347 7280 -
all-7668 -
obs--99.93 %

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