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- PDB-5mw0: Complex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (... -

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Basic information

Entry
Database: PDB / ID: 5mw0
TitleComplex between the Leucine Zipper (LZ) and Centrosomin-motif 2 (CM2) domains of Drosophila melanogaster Centrosomin (Cnn) - L535E mutant form
Components(Centrosomin) x 2
KeywordsCELL CYCLE / Centrosome / Centriole / Coiled-coil / Mitosis
Function / homology
Function and homology information


photoreceptor cell morphogenesis / pole cell formation / regulation of Golgi organization / asymmetric cell division / regulation of centriole-centriole cohesion / midgut development / asymmetric neuroblast division / peripheral nervous system development / embryonic cleavage / centrosome cycle ...photoreceptor cell morphogenesis / pole cell formation / regulation of Golgi organization / asymmetric cell division / regulation of centriole-centriole cohesion / midgut development / asymmetric neuroblast division / peripheral nervous system development / embryonic cleavage / centrosome cycle / motile cilium / pericentriolar material / centriole replication / centriole / central nervous system development / mitotic spindle organization / meiotic cell cycle / spindle pole / molecular adaptor activity / ciliary basal body / centrosome / perinuclear region of cytoplasm / Golgi apparatus
Similarity search - Function
: / Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFeng, Z. / Johnson, S. / Raff, J.W. / Lea, S.M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust10457 United Kingdom
Wellcome Trust100298 United Kingdom
CitationJournal: Cell / Year: 2017
Title: Structural Basis for Mitotic Centrosome Assembly in Flies.
Authors: Feng, Z. / Caballe, A. / Wainman, A. / Johnson, S. / Haensele, A.F.M. / Cottee, M.A. / Conduit, P.T. / Lea, S.M. / Raff, J.W.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomin
C: Centrosomin
D: Centrosomin
B: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5955
Polymers29,5304
Non-polymers651
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-112 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.769, 43.930, 68.640
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Centrosomin / Protein arrow


Mass: 8198.428 Da / Num. of mol.: 2 / Fragment: CM2 domain, UNP Residues 1082-1148
Source method: isolated from a genetically manipulated source
Details: Centrosomin CM2 domain residues 1082-1148 / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pLip / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P54623
#2: Protein Centrosomin / Protein arrow


Mass: 6566.411 Da / Num. of mol.: 2 / Fragment: LZ domain, UNP Residues 490-544 / Mutation: L535E
Source method: isolated from a genetically manipulated source
Details: Centrosomin LZ domain residues 490-544 (L535E mutant)
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pETM44 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): B834 / References: UniProt: P54623
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 15%(w/v) PEG4K, 0.2M imidazole malate pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2→31.19 Å / Num. obs: 17198 / % possible obs: 97.2 % / Redundancy: 3 % / CC1/2: 0.992 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.046 / Net I/σ(I): 6.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1246 / CC1/2: 0.521 / Rpim(I) all: 0.222 / % possible all: 97.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5mvw

5mvw


Resolution: 2→31.187 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.96
RfactorNum. reflection% reflection
Rfree0.2641 883 5.16 %
Rwork0.2374 --
obs0.2389 17103 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→31.187 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1797 0 1 142 1940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051812
X-RAY DIFFRACTIONf_angle_d0.5742419
X-RAY DIFFRACTIONf_dihedral_angle_d9.3781148
X-RAY DIFFRACTIONf_chiral_restr0.035284
X-RAY DIFFRACTIONf_plane_restr0.003310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12530.33581460.29782656X-RAY DIFFRACTION97
2.1253-2.28940.32421240.25382736X-RAY DIFFRACTION96
2.2894-2.51970.27041650.24032658X-RAY DIFFRACTION97
2.5197-2.8840.2791610.23232661X-RAY DIFFRACTION96
2.884-3.63270.23391510.22742733X-RAY DIFFRACTION98
3.6327-31.19040.2561360.23142776X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.29471.69727.50571.4291.55128.95130.2074-0.4401-0.0181-0.0891-0.18270.03270.4235-0.6054-0.03490.36480.03150.00440.3171-0.04050.3705-30.69483.4693-6.6415
23.17190.95192.14363.33171.60625.342-0.1515-0.41211.0460.8949-0.4270.0134-0.9516-0.24740.39470.5334-0.0464-0.01280.3094-0.03720.3802-6.616613.259929.7673
36.5416-1.19236.46340.6123-1.37226.7015-0.15250.370.29690.0067-0.11560.0178-0.16020.55280.29050.32870.03530.02530.3370.00550.3194-27.30356.958-9.9544
45.4455-1.1522.67645.5528-2.21445.6316-0.10850.22610.17660.6644-0.3762-0.6610.21631.14560.10620.24920.04230.01120.28210.01640.35870.0782-2.613323.3318
56.9671-2.03726.70160.9451-1.89376.3701-1.4894-0.30071.57750.2691-0.0603-0.6527-2.5080.51951.26460.9935-0.1808-0.02311.4422-0.08730.900720.904211.423161.0754
67.86552.51786.37384.10032.3466.34210.0463-0.521-0.17190.27510.0070.0735-0.14490.09580.00330.3486-0.00470.06270.41540.04090.2808-2.86073.350634.9527
77.77251.6582.7971.32771.82913.60760.86380.31030.15970.5063-0.86170.50561.7613-0.39520.02470.85170.07820.0621.25240.11520.977724.13970.714760.3388
84.9724-2.95944.45281.7526-2.5216.77210.04990.0879-0.4730.1160.02170.0464-0.59661.26580.07340.3661-0.0642-0.02920.55120.07590.47044.44196.919229.7064
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1079 through 1122 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1123 through 1140 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1081 through 1120 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1121 through 1140 )
5X-RAY DIFFRACTION5chain 'C' and (resid 496 through 517 )
6X-RAY DIFFRACTION6chain 'C' and (resid 518 through 544 )
7X-RAY DIFFRACTION7chain 'D' and (resid 494 through 517)
8X-RAY DIFFRACTION8chain 'D' and (resid 518 through 544 )

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