[English] 日本語
Yorodumi
- PDB-5td8: Crystal structure of an Extended Dwarf Ndc80 Complex -

+
Open data


ID or keywords:

Loading...

-
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 / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore ...centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / outer kinetochore / 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) ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more