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- PDB-5td8: Crystal structure of an Extended Dwarf Ndc80 Complex -

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Basic information

Entry
Database: PDB / ID: 5td8
TitleCrystal structure of an Extended Dwarf Ndc80 Complex
Components
  • (Kinetochore protein ...) x 4
  • nanobody
KeywordsREPLICATION / RWD / CH / coiled-coil / tetramer / Ndc80 / Kinetochore / NANOBODY
Function / homology
Function and homology information


centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body ...centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / cell division / protein-containing complex binding / identical protein binding / nucleus
Similarity search - Function
Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / HEC/Ndc80p family / Domain of unknown function (DUF5595) / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80
Similarity search - Domain/homology
: / Kinetochore protein NUF2 / Kinetochore protein SPC25 / Kinetochore protein NDC80 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 7.531 Å
AuthorsValverde, R. / Ingram, J. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Cell Rep / Year: 2016
Title: Conserved Tetramer Junction in the Kinetochore Ndc80 Complex.
Authors: Valverde, R. / Ingram, J. / Harrison, S.C.
History
DepositionSep 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinetochore protein NDC80
B: Kinetochore protein NUF2
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25
E: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,63911
Polymers100,4365
Non-polymers1,2046
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16210 Å2
ΔGint-288 kcal/mol
Surface area45220 Å2
Unit cell
Length a, b, c (Å)226.825, 226.825, 237.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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Kinetochore protein ... , 4 types, 4 molecules ABCD

#1: Protein Kinetochore protein NDC80 / 80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with ...80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with DMC1 protein 3


Mass: 33256.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NDC80, HEC1, TID3, YIL144W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40460
#2: Protein Kinetochore protein NUF2


Mass: 23246.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: NUF2, YOL069W
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P33895
#3: Protein Kinetochore protein SPC24


Mass: 13469.254 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First three residues not resolved in electron density map
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC24, YMR117C, YM9718.16C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q04477
#4: Protein Kinetochore protein SPC25


Mass: 14568.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SPC25, YER018C
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P40014

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Antibody / Non-polymers , 2 types, 7 molecules E

#5: Antibody nanobody


Mass: 15894.382 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#6: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg

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Details

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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG 4,000, 0.1 M CHES, pH 9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.008 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 7.53→113.413 Å / Num. obs: 4140 / % possible obs: 100 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 14
Reflection shellResolution: 7.53→7.81 Å / Redundancy: 15 % / Rmerge(I) obs: 2.17 / Mean I/σ(I) obs: 1.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata scaling
Aimlessdata scaling
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 7.531→113.413 Å / SU ML: 0.95 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3283 203 4.9 %
Rwork0.3124 --
obs0.3132 4139 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 7.531→113.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 6 0 6435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046545
X-RAY DIFFRACTIONf_angle_d0.7548802
X-RAY DIFFRACTIONf_dihedral_angle_d11.913989
X-RAY DIFFRACTIONf_chiral_restr0.044972
X-RAY DIFFRACTIONf_plane_restr0.0051143
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)
10.17740.0597-0.0465-0.0009-0.0062-0.008-0.082-0.05-0.19220.14930.10050.1674-0.0814-0.35320.19460.1898-0.5397-0.55941.2113-0.22130.878248.739995.120329.9164
20.03590.09810.02660.1918-0.00750.1048-0.10390.2845-0.2898-0.2867-0.3726-0.1851-0.01630.0744-1.4905-1.0552-1.4130.64861.0541-0.64650.9143260.965392.685925.3459
30.8582-0.7367-0.31290.67570.12820.22150.77360.52550.5564-1.30920.38350.496-0.0899-0.09280.13931.918-0.65090.20091.57250.01171.982247.8647107.090815.8112
4-0.0303-0.66360.2772-0.14490.068-0.54420.1596-0.1097-2.03480.1558-0.1818-0.7360.2251-0.0742-0.35880.18320.769-0.27130.3187-0.8190.342224.9311133.7453-13.5983
50.1422-0.0364-0.04680.0778-0.0130.1258-0.00430.0933-0.0982-0.1204-0.0789-0.07060.20350.13530.02890.4150.37530.67120.28030.39640.8903273.5989104.5869-7.9
60.13450.109-0.26090.0959-0.20250.5210.0033-0.0075-0.09470.023-0.3479-0.01680.27921.04850.03011.80430.3911-0.73871.0233-0.07561.1717268.5774105.95291.4447
70.79150.4167-0.04550.62640.13620.9828-0.7965-0.7263-0.32130.1965-1.0753-0.33341.06341.0148-5.80330.39040.1807-0.4860.62390.70151.1682245.328121.7699-1.864
80.04840.0065-0.03340.004-0.01710.04590.09030.1662-0.342-0.18980.04510.07670.28930.7555-0.06331.00730.11540.09060.9471-0.43790.8892218.1541156.3283-19.2665
90.4314-0.4498-0.21230.27030.1191-0.01440.1019-0.30560.49970.26420.224-0.2655-0.3288-0.22830.09021.20470.69070.8080.5627-0.21080.5363188.0436196.0228-11.9599
100.0812-0.05040.07440.0282-0.03440.0593-0.0721-0.2663-0.0536-0.0119-0.1015-0.04510.2599-0.0789-0.62510.8245-0.0490.0090.490.77820.9132160.2169200.3956-16.5745
110.28530.2041-0.16470.1971-0.16180.13890.0964-0.21250.02920.2812-0.12480.0445-0.1027-0.0501-0.21680.1154-0.4686-0.00580.2071-0.1626-0.16160.4211208.5888-21.1737
120.89870.42990.0930.560.13350.7437-0.211-0.2070.39120.0414-0.03550.31450.03560.5728-0.51270.09080.40770.1650.23950.19020.4073193.6653181.2284-10.2304
130.1221-0.08410.14080.0686-0.06540.20050.0505-0.33050.1076-0.1009-0.2313-0.0734-0.14540.198-0.16391.520.22810.59721.6966-0.09160.9192179.8963217.8433-12.391
140.0134-0.16180.05762.3724-1.03430.4515-0.02480.0750.09070.72480.06190.0622-0.2822-0.14540.1430.687-0.3457-0.36720.85190.62290.9998174.6429222.114-13.4449
150.1227-0.013-0.04380.01090.01070.01570.06150.02120.0622-0.146-0.0043-0.0313-0.22930.04150.04152.05410.30130.29720.9056-0.75831.2636165.2652224.0112-5.2963
160.0469-0.0309-0.07590.01220.04120.1175-0.118-0.03240.0008-0.07040.00190.0531-0.06010.027-0.24140.94711.0414-0.01061.1966-0.26050.3653165.6279219.8386-15.9175
170.0002-0.00280.00070.06560.02260.0032-0.00410.0128-0.0118-0.0070.0398-0.0958-0.03470.00030.02950.4292-0.4265-0.28660.1999-0.24070.445203.1197151.9217-33.8209
180.07590.04090.05710.06440.07240.1317-0.35690.1034-0.1743-0.1057-0.058-0.10840.10230.0629-0.36351.2372-0.44220.21960.95070.2530.534193.6001162.384-33.3096
190.00410.0305-0.0060.0502-0.02230.0098-0.0292-0.05120.10350.017-0.0671-0.0126-0.12660.0472-0.04770.3642-0.139-0.37770.1160.05650.3781207.4313161.6139-35.0031
200.3167-0.20830.17450.1876-0.13150.1399-0.00370.26680.0436-0.1872-0.11520.2091-0.01860.1662-0.38480.48210.1316-0.62130.2812-0.09050.1259207.2587168.5125-35.0942
210.0632-0.0068-0.06390.00850.00910.06030.00830.11150.0113-0.0449-0.07120.0236-0.0085-0.1109-0.26850.98840.99130.26380.67880.22760.1216202.319161.4598-26.063
220.22560.0630.17940.02130.04860.15040.27270.25590.13530.14130.0667-0.01490.3743-0.2740.38081.299-0.10820.11970.61330.27970.6005198.0192167.3056-38.6415
230.10290.0859-0.02740.1052-0.07770.08570.0389-0.06260.1041-0.0148-0.0178-0.052-0.02840.00290.21670.58520.86060.28230.8291-0.34931.4564212.8713156.0684-36.1034
240.04250.01060.00280.01050.01430.028-0.0189-0.01550.0456-0.0221-0.0350.0227-0.1361-0.03360.00840.8111-0.4064-0.35920.5344-0.30111.1795191.2904165.2359-41.6967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 115 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 212 )
3X-RAY DIFFRACTION3chain 'A' and (resid 213 through 266 )
4X-RAY DIFFRACTION4chain 'A' and (resid 267 through 682 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 32 )
6X-RAY DIFFRACTION6chain 'B' and (resid 33 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 451 )
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 23 )
9X-RAY DIFFRACTION9chain 'C' and (resid 24 through 181 )
10X-RAY DIFFRACTION10chain 'C' and (resid 182 through 199 )
11X-RAY DIFFRACTION11chain 'C' and (resid 200 through 213 )
12X-RAY DIFFRACTION12chain 'D' and (resid 2 through 145 )
13X-RAY DIFFRACTION13chain 'D' and (resid 146 through 158 )
14X-RAY DIFFRACTION14chain 'D' and (resid 159 through 189 )
15X-RAY DIFFRACTION15chain 'D' and (resid 190 through 205 )
16X-RAY DIFFRACTION16chain 'D' and (resid 206 through 221 )
17X-RAY DIFFRACTION17chain 'E' and (resid 3 through 8 )
18X-RAY DIFFRACTION18chain 'E' and (resid 9 through 26 )
19X-RAY DIFFRACTION19chain 'E' and (resid 27 through 40 )
20X-RAY DIFFRACTION20chain 'E' and (resid 41 through 68 )
21X-RAY DIFFRACTION21chain 'E' and (resid 69 through 84 )
22X-RAY DIFFRACTION22chain 'E' and (resid 85 through 99 )
23X-RAY DIFFRACTION23chain 'E' and (resid 100 through 121 )
24X-RAY DIFFRACTION24chain 'E' and (resid 122 through 128 )

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