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- PDB-7fad: Crystal structure of Xenopus GCP2-N terminal domain and Mzt2 -

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Basic information

Entry
Database: PDB / ID: 7fad
TitleCrystal structure of Xenopus GCP2-N terminal domain and Mzt2
Components
  • Gamma-tubulin complex component
  • Mitotic-spindle organizing protein 2B
KeywordsSTRUCTURAL PROTEIN / Microtubule nucleation
Function / homology
Function and homology information


Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / gamma-tubulin ring complex / microtubule nucleation / gamma-tubulin binding / microtubule organizing center / spindle pole / spindle / microtubule / centrosome / cytoplasm
Similarity search - Function
MOZART2 family / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal
Similarity search - Domain/homology
Mitotic-spindle organizing protein 2B / Gamma-tubulin complex component
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Xenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.204 Å
AuthorsShankar, S. / Huang, T.L. / Hsia, K.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
Academia Sinica (Taiwan) Taiwan
CitationJournal: Cell Rep / Year: 2022
Title: A gamma-tubulin complex independent pathway could suppress ciliogenesis by promoting cilia disassembly
Authors: Shankar, S. / Hsu, Z.T. / Ezquerra, A. / Li, C.C. / Huang, T.L. / Coyaud, E. / Viais, R. / Grauffel, C. / Raught, B. / Lim, C. / Luders, J. / Tsai, S.Y. / Hsia, K.C.
History
DepositionJul 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Feb 15, 2023Group: Database references / Category: citation / Item: _citation.title
Revision 1.3May 29, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Assembly

Deposited unit
A: Gamma-tubulin complex component
B: Mitotic-spindle organizing protein 2B
C: Gamma-tubulin complex component
D: Mitotic-spindle organizing protein 2B
E: Gamma-tubulin complex component
F: Mitotic-spindle organizing protein 2B


Theoretical massNumber of molelcules
Total (without water)88,1576
Polymers88,1576
Non-polymers00
Water0
1
A: Gamma-tubulin complex component
B: Mitotic-spindle organizing protein 2B


Theoretical massNumber of molelcules
Total (without water)29,3862
Polymers29,3862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-44 kcal/mol
Surface area8570 Å2
MethodPISA
2
C: Gamma-tubulin complex component
D: Mitotic-spindle organizing protein 2B


Theoretical massNumber of molelcules
Total (without water)29,3862
Polymers29,3862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-44 kcal/mol
Surface area8710 Å2
MethodPISA
3
E: Gamma-tubulin complex component
F: Mitotic-spindle organizing protein 2B


Theoretical massNumber of molelcules
Total (without water)29,3862
Polymers29,3862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-46 kcal/mol
Surface area8680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.878, 125.099, 204.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain B and (resseq 44:47 or resseq 49:63 or (resid...
21(chain D and (resseq 44:47 or resseq 49:63 or (resid...
31(chain F and (resseq 44:47 or resseq 49:63 or (resid...
12(chain A and (resseq 0:20 or resseq 24:27 or (resid...
22(chain C and (resseq 0:20 or resseq 24:27 or (resid...
32(chain E and (resseq 0:20 or resseq 24:27 or (resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALPROPRO(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB44 - 4748 - 51
121GLUGLUILEILE(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB49 - 6353 - 67
131ASPASPASPASP(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB6468
141VALVALALAALA(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB44 - 9348 - 97
151VALVALALAALA(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB44 - 9348 - 97
161VALVALALAALA(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB44 - 9348 - 97
171VALVALALAALA(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB44 - 9348 - 97
181VALVALALAALA(chain B and (resseq 44:47 or resseq 49:63 or (resid...BB44 - 9348 - 97
211VALVALPROPRO(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD44 - 4748 - 51
221GLUGLUILEILE(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD49 - 6353 - 67
231ASPASPASPASP(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD6468
241VALVALALAALA(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD44 - 9348 - 97
251VALVALALAALA(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD44 - 9348 - 97
261VALVALALAALA(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD44 - 9348 - 97
271VALVALALAALA(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD44 - 9348 - 97
281VALVALALAALA(chain D and (resseq 44:47 or resseq 49:63 or (resid...DD44 - 9348 - 97
311VALVALPROPRO(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF44 - 4748 - 51
321GLUGLUILEILE(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF49 - 6353 - 67
331ASPASPASPASP(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF6468
341VALVALALAALA(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF44 - 9348 - 97
351VALVALALAALA(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF44 - 9348 - 97
361VALVALALAALA(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF44 - 9348 - 97
371VALVALALAALA(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF44 - 9348 - 97
381VALVALALAALA(chain F and (resseq 44:47 or resseq 49:63 or (resid...FF44 - 9348 - 97
112SERSERPHEPHE(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 205 - 25
122GLYGLYVALVAL(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA24 - 2729 - 32
132TYRTYRTYRTYR(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA2833
142SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
152SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
162SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
172SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
182SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
192SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
1102SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
1112SERSERALAALA(chain A and (resseq 0:20 or resseq 24:27 or (resid...AA0 - 1065 - 111
212SERSERPHEPHE(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 205 - 25
222GLYGLYVALVAL(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC24 - 2729 - 32
232TYRTYRTYRTYR(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC2833
242SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
252SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
262SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
272SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
282SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
292SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
2102SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
2112SERSERGLUGLU(chain C and (resseq 0:20 or resseq 24:27 or (resid...CC0 - 1075 - 112
312SERSERPHEPHE(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 205 - 25
322GLYGLYVALVAL(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE24 - 2729 - 32
332TYRTYRTYRTYR(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE2833
342SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
352SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
362SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
372SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
382SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
392SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
3102SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110
3112SERSERLYSLYS(chain E and (resseq 0:20 or resseq 24:27 or (resid...EE0 - 1055 - 110

NCS ensembles :
ID
1
2

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Components

#1: Protein Gamma-tubulin complex component


Mass: 19041.717 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: tubgcp2.L, tubgcp2, tubgcp2-prov / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DDJ4
#2: Protein Mitotic-spindle organizing protein 2B / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2B


Mass: 10344.030 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: mzt2b, fam128, mozart2, TEgg010b01.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q28DB1

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Description: The entry contains friedel pairs in I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium formate pH 7, 12% PEG 3350

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.17→20 Å / Num. obs: 18101 / % possible obs: 98.5 % / Redundancy: 6.5 % / Rrim(I) all: 0.134 / Net I/σ(I): 25.33
Reflection shellResolution: 3.17→3.29 Å / Num. unique obs: 1608 / CC1/2: 0.909 / % possible all: 89.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.204→19.957 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.51 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2374 3314 9.96 %
Rwork0.2062 29954 -
obs0.2094 17682 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 195.68 Å2 / Biso min: 63.81 Å2
Refinement stepCycle: final / Resolution: 3.204→19.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3665 0 0 0 3665
Num. residues----456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123712
X-RAY DIFFRACTIONf_angle_d1.5985000
X-RAY DIFFRACTIONf_chiral_restr0.075602
X-RAY DIFFRACTIONf_plane_restr0.008623
X-RAY DIFFRACTIONf_dihedral_angle_d15.3992304
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B667X-RAY DIFFRACTION10.697TORSIONAL
12D667X-RAY DIFFRACTION10.697TORSIONAL
13F667X-RAY DIFFRACTION10.697TORSIONAL
21A1282X-RAY DIFFRACTION10.697TORSIONAL
22C1282X-RAY DIFFRACTION10.697TORSIONAL
23E1282X-RAY DIFFRACTION10.697TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.204-3.24910.46621190.3602114490
3.2491-3.29740.39871320.3449114493
3.2974-3.34870.40681380.3479123796
3.3487-3.40330.38631370.3488123398
3.4033-3.46170.33971380.2959126299
3.4617-3.52430.3861410.29521259100
3.5243-3.59170.34121380.26281244100
3.5917-3.66460.28061390.25951264100
3.6646-3.74380.27441370.25771283100
3.7438-3.83030.33971410.24771250100
3.8303-3.92540.30281400.24921285100
3.9254-4.03070.28711320.23471227100
4.0307-4.14820.25771410.20561255100
4.1482-4.28090.25021410.19151275100
4.2809-4.43230.22781420.19421257100
4.4323-4.60760.21671350.17125499
4.6076-4.81450.17191420.15371265100
4.8145-5.06440.19831460.15631271100
5.0644-5.37590.23121380.17361241100
5.3759-5.78160.1931431265100
5.7816-6.34640.20781420.2071265100
6.3464-7.22630.21461340.20911250100
7.2263-8.96490.18691410.1711271100
8.9649-19.9570.17091370.156125399
Refinement TLS params.Method: refined / Origin x: 31.0268 Å / Origin y: 28.1202 Å / Origin z: 239.8286 Å
111213212223313233
T0.8915 Å2-0.0468 Å20.0072 Å2-0.5555 Å2-0.0335 Å2--0.6201 Å2
L0.8927 °20.2074 °2-0.3605 °2-1.7616 °2-0.9901 °2--1.9973 °2
S-0.1322 Å °0.2335 Å °-0.2302 Å °-0.7149 Å °-0.0279 Å °-0.0597 Å °0.5797 Å °-0.0238 Å °0.1597 Å °
Refinement TLS groupSelection details: all

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