[English] 日本語
Yorodumi
- PDB-5jvp: The neck-linker and alpha 7 helix of Homo sapiens CENP-E -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jvp
TitleThe neck-linker and alpha 7 helix of Homo sapiens CENP-E
ComponentsChimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic chromosome movement towards spindle pole / mitotic spindle astral microtubule end / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / protein localization to microtubule ...lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic chromosome movement towards spindle pole / mitotic spindle astral microtubule end / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / protein localization to microtubule / kinetochore binding / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / Kinesins / regulation of mitotic metaphase/anaphase transition / protein localization to centrosome / COPI-dependent Golgi-to-ER retrograde traffic / microtubule organizing center / negative regulation of microtubule polymerization / microtubule motor activity / mitotic metaphase chromosome alignment / intercellular bridge / microtubule-based movement / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / chromosome, centromeric region / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / positive regulation of protein kinase activity / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / AURKA Activation by TPX2 / mitotic spindle organization / ciliary basal body / chromosome segregation / RHO GTPases Activate Formins / protein localization / mitotic spindle / kinetochore / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / cell migration / mitotic cell cycle / chromosome / midbody / microtubule binding / microtubule / molecular adaptor activity / cadherin binding / cell division / focal adhesion / intracellular membrane-bounded organelle / centrosome / protein kinase binding / Golgi apparatus / RNA binding / ATP binding / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Kinesin motor domain signature. ...EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Kinesin motor domain signature. / Calponin homology (CH) domain profile. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Centromere-associated protein E / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPhillips, R.K. / Rayment, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM54141 United States
National Science Foundation (NSF, United States)DGE-0718123 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil.
Authors: Phillips, R.K. / Peter, L.G. / Gilbert, S.P. / Rayment, I.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
C: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
E: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
F: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6269
Polymers64,2886
Non-polymers3373
Water8,755486
1
A: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules

A: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6544
Polymers21,4292
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4470 Å2
ΔGint-40 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules

B: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6544
Polymers21,4292
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area4340 Å2
ΔGint-42 kcal/mol
Surface area13410 Å2
MethodPISA
3
C: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5423
Polymers21,4292
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-39 kcal/mol
Surface area13090 Å2
MethodPISA
4
E: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
F: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)21,4292
Polymers21,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-42 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.609, 100.609, 107.627
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-101-

CD

21B-228-

HOH

31B-277-

HOH

41B-306-

HOH

-
Components

#1: Protein
Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1 / / Centromere protein E / CENP-E / Kinesin-related protein CENPE / APC-binding protein EB1 / End- ...Centromere protein E / CENP-E / Kinesin-related protein CENPE / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 10714.730 Da / Num. of mol.: 6
Fragment: UNP Q02224 residues 336-375,UNP Q15691 residues 210-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPE, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02224, UniProt: Q15691
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% (w/v) MEPEG 2000, 175 mM Li2SO4, 100 mM MES pH 6.0, 1 mM CdCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.1→45.786 Å / Num. obs: 71015 / % possible obs: 100 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 12.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→45.785 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2739 3521 4.96 %
Rwork0.2372 --
obs0.239 71015 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→45.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 3 486 4814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024372
X-RAY DIFFRACTIONf_angle_d0.4275858
X-RAY DIFFRACTIONf_dihedral_angle_d18.2362772
X-RAY DIFFRACTIONf_chiral_restr0.035659
X-RAY DIFFRACTIONf_plane_restr0.002771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12880.28091370.26322651X-RAY DIFFRACTION99
2.1288-2.15920.32011460.27062676X-RAY DIFFRACTION100
2.1592-2.19150.32191420.2582715X-RAY DIFFRACTION100
2.1915-2.22570.32231480.26762733X-RAY DIFFRACTION100
2.2257-2.26220.35151400.25372660X-RAY DIFFRACTION100
2.2622-2.30120.35171400.27012742X-RAY DIFFRACTION100
2.3012-2.3430.28481360.25772654X-RAY DIFFRACTION100
2.343-2.38810.34091500.26012701X-RAY DIFFRACTION100
2.3881-2.43680.31431420.26592680X-RAY DIFFRACTION100
2.4368-2.48980.36551400.26242741X-RAY DIFFRACTION100
2.4898-2.54770.30641420.2482672X-RAY DIFFRACTION100
2.5477-2.61150.28731430.25492727X-RAY DIFFRACTION100
2.6115-2.68210.31441440.25062742X-RAY DIFFRACTION100
2.6821-2.7610.26791440.24362686X-RAY DIFFRACTION100
2.761-2.85010.38961360.24682683X-RAY DIFFRACTION100
2.8501-2.95190.2991290.2332714X-RAY DIFFRACTION100
2.9519-3.07010.28121440.23882685X-RAY DIFFRACTION100
3.0701-3.20980.27411360.24022717X-RAY DIFFRACTION100
3.2098-3.37890.25481460.22752707X-RAY DIFFRACTION100
3.3789-3.59060.30211420.23732730X-RAY DIFFRACTION100
3.5906-3.86770.22761350.22372703X-RAY DIFFRACTION100
3.8677-4.25660.19461420.19562691X-RAY DIFFRACTION100
4.2566-4.8720.22741380.1942700X-RAY DIFFRACTION100
4.872-6.13590.23061380.24632701X-RAY DIFFRACTION100
6.1359-45.79580.22331410.22842683X-RAY DIFFRACTION99
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)
11.61071.2013-0.07311.7014-0.30550.64410.2783-0.0959-0.09080.1073-0.1353-0.1272-0.05690.0798-0.04750.0959-0.03950.0990.1167-0.02590.066942.080675.35551.2643
24.92021.2306-0.24780.80330.71491.85780.2062-0.0213-0.6285-0.2309-0.0760.16050.2147-0.0738-0.0580.41450.0392-0.19590.1181-0.11450.545529.762543.042-7.9287
31.7884-1.94380.22533.6728-0.33780.3426-0.0335-0.01460.07410.10840.0506-0.0904-0.0387-0.0594-0.00530.16050.01720.07980.03950.03280.056553.271979.6774-16.363
40.62140.11340.17940.93520.05161.4166-0.0620.0742-0.5111-0.00790.0585-0.10510.36330.3223-0.05120.21660.14440.13770.2353-0.08110.442576.920250.6532-24.9942
54.31140.3128-1.31430.1347-0.15540.4739-0.131-0.41090.155-0.070.0083-0.0039-0.05430.1003-0.03230.20420.05110.01330.2796-0.12820.099438.437929.872319.0178
60.35620.10270.28631.15660.13621.70750.0142-0.1870.0678-0.0758-0.10460.36290.1152-0.56930.57520.346-0.193-0.04640.5626-0.29820.45560.567421.294911.5195
72.6069-0.9647-1.99271.21880.9161.56020.24330.2044-0.2902-0.2685-0.21420.26670.0404-0.35560.00730.18220.0557-0.09770.39480.09280.235872.510428.511630.4914
84.27111.32511.46050.60270.20550.7578-0.21380.6674-0.408-0.15070.086-0.0619-0.13690.08340.05070.25960.021-0.02080.2331-0.04790.076433.827127.047715.1007
93.91080.5489-0.97462.66711.31683.33020.15190.27380.1219-0.0492-0.25420.4029-0.1103-0.63950.27870.31920.16490.01390.399-0.17550.25232.992530.645926.1679
102.85212.94211.12783.68931.31220.4638-0.45070.2091-0.0674-0.35630.2422-0.0366-0.0328-0.0463-0.00780.3871-0.07840.08390.2921-0.08620.1571-3.810849.8267-1.459
111.49151.0758-0.98911.5129-0.1171.7818-0.36260.0796-0.6816-0.285-0.0357-0.25370.6578-0.01970.4320.6865-0.1770.42520.4624-0.13950.6816-29.027223.34556.7832
120.96941.518-0.39742.4655-0.59590.12580.1355-0.2049-0.08390.3445-0.3252-0.10470.03860.0248-0.03660.4668-0.1270.15150.3272-0.01320.235-5.391851.78781.3086
130.9636-0.01780.12840.4428-0.7131.64990.1285-0.06280.07780.22720.1528-0.02120.49730.1060.51910.6799-0.03650.2180.4115-0.22620.5268-21.057319.5692-8.3682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 90 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 63 )
4X-RAY DIFFRACTION4chain 'B' and (resid 64 through 90 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 62 )
6X-RAY DIFFRACTION6chain 'C' and (resid 63 through 90 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 7 )
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 64 )
9X-RAY DIFFRACTION9chain 'D' and (resid 65 through 90 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 63 )
11X-RAY DIFFRACTION11chain 'E' and (resid 64 through 90 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 62 )
13X-RAY DIFFRACTION13chain 'F' and (resid 63 through 89 )

+
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