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- PDB-3vza: Crystal structure of the chicken Spc24-Spc25 globular domain in c... -

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Basic information

Entry
Database: PDB / ID: 3vza
TitleCrystal structure of the chicken Spc24-Spc25 globular domain in complex with CENP-T peptide
Components
  • Centromere protein T
  • Spc24 protein
  • Uncharacterized protein
KeywordsCELL CYCLE / RWD domain / kinetochore component / chromosome segregation / Ndc80 complex
Function / homology
Function and homology information


Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Ndc80 complex / kinetochore => GO:0000776 / kinetochore assembly ...Mitotic Prometaphase / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Separation of Sister Chromatids / Deposition of new CENPA-containing nucleosomes at the centromere / Ndc80 complex / kinetochore => GO:0000776 / kinetochore assembly / chromosome segregation / kinetochore / mitotic cell cycle / cell cycle / protein heterodimerization activity / cell division / DNA binding / nucleus
Similarity search - Function
Chromosome segregation protein Spc25 / Chromosome segregation protein Spc25, C-terminal / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 ...Chromosome segregation protein Spc25 / Chromosome segregation protein Spc25, C-terminal / Kinetochore protein Spc25 / Chromosome segregation protein Spc25 / Centromere protein T / Centromere kinetochore component CENP-T, N-terminal domain / Centromere kinetochore component CENP-T N-terminus / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80 / Copper Amine Oxidase; Chain A, domain 1 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone-fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinetochore protein SPC25 / Centromere protein T / Kinetochore protein Spc24
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsNishino, T. / Fukagawa, T.
CitationJournal: Embo J. / Year: 2013
Title: CENP-T provides a structural platform for outer kinetochore assembly
Authors: Nishino, T. / Rago, F. / Hori, T. / Tomii, K. / Cheeseman, I.M. / Fukagawa, T.
History
DepositionOct 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Uncharacterized protein
D: Spc24 protein
A: Uncharacterized protein
C: Spc24 protein
E: Centromere protein T
F: Centromere protein T


Theoretical massNumber of molelcules
Total (without water)50,6856
Polymers50,6856
Non-polymers00
Water6,431357
1
B: Uncharacterized protein
D: Spc24 protein
F: Centromere protein T


Theoretical massNumber of molelcules
Total (without water)25,3423
Polymers25,3423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-39 kcal/mol
Surface area10390 Å2
MethodPISA
2
A: Uncharacterized protein
C: Spc24 protein
E: Centromere protein T


Theoretical massNumber of molelcules
Total (without water)25,3423
Polymers25,3423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-38 kcal/mol
Surface area10230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.321, 61.321, 111.275
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN B AND (RESSEQ 134:231 )
21CHAIN A AND (RESSEQ 134:231 )
12CHAIN D AND (RESSEQ 134:195 )
22CHAIN C AND (RESSEQ 134:195 )
13CHAIN E AND (RESSEQ 63:93 )
23CHAIN F AND (RESSEQ 63:93 )

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGLYSLYSCHAIN B AND (RESSEQ 134:231 )BA134 - 2315 - 102
21ARGARGLYSLYSCHAIN A AND (RESSEQ 134:231 )AC134 - 2315 - 102
12ALAALATRPTRPCHAIN D AND (RESSEQ 134:195 )DB134 - 19512 - 73
22ALAALATRPTRPCHAIN C AND (RESSEQ 134:195 )CD134 - 19512 - 73
13ASNASNGLNGLNCHAIN E AND (RESSEQ 63:93 )EE63 - 933 - 33
23ASNASNGLNGLNCHAIN F AND (RESSEQ 63:93 )FF63 - 933 - 33

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Uncharacterized protein / Spc25 protein


Mass: 12466.171 Da / Num. of mol.: 2 / Fragment: RWD domain, globular domain, UNP residues 132-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPC25 / Production host: Escherichia coli (E. coli) / References: UniProt: E1C4Y2
#2: Protein Spc24 protein /


Mass: 8455.313 Da / Num. of mol.: 2 / Fragment: RWD domain, globular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: R4GRT4*PLUS
#3: Protein/peptide Centromere protein T / / CENP-T


Mass: 4421.001 Da / Num. of mol.: 2
Fragment: CENP-T Spc24-25 interacting region, residues 63-98
Mutation: T72D, S88D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CENPT / Production host: Escherichia coli (E. coli) / References: UniProt: F1NPG5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR CHAIN D, C DOES NOT CURRENTLY EXIST.

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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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.02M Na/K phosphate, 0.1M Bis Tris propane, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. all: 36984 / Num. obs: 36934 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 26.09 Å2 / Rsym value: 0.06 / Net I/σ(I): 30.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.55 / Rsym value: 0.536 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3vz9

3vz9


Resolution: 1.898→30.409 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8737 / SU ML: 0.45 / σ(F): 1.97 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1994 5.4 %random
Rwork0.1669 ---
all0.1695 36934 --
obs0.1695 36934 99.87 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.654 Å2 / ksol: 0.347 e/Å3
Displacement parametersBiso max: 133.01 Å2 / Biso mean: 35.375 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.1906 Å20 Å20 Å2
2---0.1906 Å2-0 Å2
3---1.6568 Å2
Refinement stepCycle: LAST / Resolution: 1.898→30.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 357 3532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0223253
X-RAY DIFFRACTIONf_angle_d1.9234402
X-RAY DIFFRACTIONf_chiral_restr0.146471
X-RAY DIFFRACTIONf_plane_restr0.012572
X-RAY DIFFRACTIONf_dihedral_angle_d15.5481224
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B820X-RAY DIFFRACTIONPOSITIONAL0.093
12A820X-RAY DIFFRACTIONPOSITIONAL0.093
21D516X-RAY DIFFRACTIONPOSITIONAL0.055
22C516X-RAY DIFFRACTIONPOSITIONAL0.055
31E247X-RAY DIFFRACTIONPOSITIONAL0.082
32F247X-RAY DIFFRACTIONPOSITIONAL0.082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8982-1.94570.23371400.221424552595100
1.9457-1.99830.24511440.201525482692100
1.9983-2.05710.19171450.1824712616100
2.0571-2.12340.21261440.166425112655100
2.1234-2.19930.21361440.173324902634100
2.1993-2.28730.23061480.164325192667100
2.2873-2.39140.26441340.170524592593100
2.3914-2.51740.16681520.169424962648100
2.5174-2.67510.22381430.17125272670100
2.6751-2.88150.24531390.175424702609100
2.8815-3.17120.22881440.166425262670100
3.1712-3.62940.20771380.162925082646100
3.6294-4.57010.18631410.140224962637100
4.5701-30.41270.22931380.17492464260299
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)
15.04310.949-1.39741.79651.02965.54990.0564-0.2669-1.0340.6351-0.0677-0.25370.85910.07340.21760.4315-0.1497-0.05670.35480.15730.49492.6185-2.822621.6963
21.79020.40490.26132.0698-0.30870.4301-0.0626-0.069-0.0794-0.0182-0.0842-0.14340.02120.05580.03110.2764-0.19080.04730.21690.05540.2161-2.16927.016521.4578
34.17442.5292-0.64335.0958-1.15650.70730.1242-0.33720.01670.2345-0.0270.0538-0.1756-0.0873-0.03160.2784-0.12840.05810.2344-0.02360.153-12.14117.067923.7746
45.07182.1015-1.10456.43173.40918.18590.1087-0.27430.28520.1902-0.09520.186-0.29350.1404-0.01640.5832-0.25360.0850.4741-0.11970.2471-0.100819.572429.585
53.64083.07853.86263.83351.82715.77910.4308-0.4750.20170.5861-0.3340.20960.0488-0.0123-0.10630.3845-0.17780.11240.2348-0.06080.2407-10.080714.801925.4803
62.15581.20230.26241.77680.47011.7294-0.02970.00180.3156-0.25370.06270.4158-0.2936-0.0922-0.01690.2938-0.07990.00750.1205-0.00940.2487-16.563312.451512.5537
76.07923.6516-1.4266.1016-0.13713.61220.1151-0.5265-0.83560.2102-0.2829-0.88970.24760.40330.12110.296-0.0980.05820.1590.05760.37335.13292.402214.73
85.41732.67360.1235.53041.39934.584-0.39460.65720.3278-0.5113-0.0373-0.2137-0.45230.67940.39970.2896-0.04570.07970.20110.09510.32458.79918.58137.2896
93.78821.81330.68394.1314-0.65163.02510.1616-0.2868-0.04980.3491-0.2463-0.3472-0.10930.3488-0.01920.3029-0.21030.08770.1565-0.01570.23543.855115.140316.4981
107.88933.9075-2.0498.33470.71845.9924-0.28680.7286-0.1164-0.74060.25070.860.0955-0.64120.14510.5175-0.0777-0.18380.2462-0.02910.3963-33.4004-16.3602-0.0702
110.4153-0.1985-0.26622.70191.60751.2162-0.03320.0631-0.0181-0.011-0.02710.15440.01910.06050.03920.3622-0.0799-0.00350.1151-0.06390.1794-22.1856-24.2448-1.3584
123.82172.50480.23188.6298-0.91661.3427-0.03020.28640.1237-0.6190.2011-0.02880.00480.1079-0.10430.3397-0.1050.06130.1836-0.03330.1527-17.3243-21.0448-1.2613
132.25180.9772-2.79272.2485-2.00995.0213-0.0134-0.07280.0511-0.2519-0.0174-0.221-0.28060.33840.05010.7177-0.21720.1180.335-0.00680.2675-13.3858-9.0258-7.7352
141.11921.9187-1.48918.4296-5.98335.7002-0.04350.0757-0.0175-0.66650.1794-0.11050.1716-0.0131-0.11290.2989-0.08250.05980.1452-0.04350.1869-14.3961-26.33051.8065
152.51651.3075-1.01663.4182-1.70913.51540.1189-0.1671-0.4115-0.0477-0.2015-0.6165-0.05070.45470.12340.2299-0.08670.02180.2052-0.0270.3168-9.1068-27.94127.3819
161.4870.8396-0.34853.3338-0.97481.30530.1454-0.1732-0.02640.2283-0.1335-0.301-0.06520.09240.19470.3078-0.220.03570.135-0.00130.1894-13.3443-21.178612.3285
173.16271.8703-0.75338.7321.96052.7508-0.0140.15280.4428-0.6674-0.15171.1704-0.2867-0.36680.07490.2914-0.1125-0.0190.1679-0.0710.3756-31.1463-12.05487.1748
183.24230.9463-0.30546.6595-0.75974.3761-0.2099-0.42160.42040.6599-0.2479-0.0178-0.7648-0.07070.46020.2861-0.0642-0.06050.2254-0.12760.358-27.6302-5.791314.6154
198.16296.22971.40266.3781-0.978.05790.00710.46350.7373-1.10630.08550.3777-1.2214-0.4803-0.13570.6501-0.041-0.07540.27950.06750.2827-23.0865-1.1415-2.4323
201.27730.81780.51761.88850.24220.3993-0.0582-0.00270.1166-0.0328-0.02460.0163-0.0574-0.0055-0.00380.3313-0.18120.06960.1137-0.08590.2388-17.751-9.4949.1456
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN B AND (RESSEQ 134:147)B134 - 147
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 148:153)B148 - 153
3X-RAY DIFFRACTION3CHAIN B AND (RESSEQ 154:169)B154 - 169
4X-RAY DIFFRACTION4CHAIN B AND (RESSEQ 170:174)B170 - 174
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 175:179)B175 - 179
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 180:223)B180 - 223
7X-RAY DIFFRACTION7CHAIN D AND (RESSEQ 137:161)D137 - 161
8X-RAY DIFFRACTION8CHAIN D AND (RESSEQ 162:174)D162 - 174
9X-RAY DIFFRACTION9CHAIN D AND (RESSEQ 175:195)D175 - 195
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 135:147)A135 - 147
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 148:158)A148 - 158
12X-RAY DIFFRACTION12CHAIN A AND (RESSEQ 159:169)A159 - 169
13X-RAY DIFFRACTION13CHAIN A AND (RESSEQ 170:175)A170 - 175
14X-RAY DIFFRACTION14CHAIN A AND (RESSEQ 176:184)A176 - 184
15X-RAY DIFFRACTION15CHAIN A AND (RESSEQ 185:206)A185 - 206
16X-RAY DIFFRACTION16CHAIN A AND (RESSEQ 207:224)A207 - 224
17X-RAY DIFFRACTION17CHAIN C AND (RESSEQ 137:161)C137 - 161
18X-RAY DIFFRACTION18CHAIN C AND (RESSEQ 162:174)C162 - 174
19X-RAY DIFFRACTION19CHAIN C AND (RESSEQ 175:181)C175 - 181
20X-RAY DIFFRACTION20CHAIN C AND (RESSEQ 182:195)C182 - 195

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